The Muslim Brotherhood’s Influence on Al-Qaeda, ISIS, and Iran

Download Full Report

Muslim Brotherhood




Before ascending to the highest positions of ISIS and al-Qaeda, Abu Bakr al-Baghdadi, Osama bin Laden, and Ayman al-Zawahiri belonged to a common ideological precursor, the Muslim Brotherhood. The trajectories of these three extremist leaders highlight the significant ideological overlap between today’s most notorious violent Islamist groups—ISIS and al-Qaeda—and the worldwide Muslim Brotherhood movement.

In commemorating the 70th anniversary of the Brotherhood, Yusuf al-Qaradawi wrote that the Brotherhood is “not only the largest Islamist movement. It is also the mother of all Islamist movements.” As the progenitor of the modern Islamist movement, the Muslim Brotherhood (i.e. the Brotherhood) has had a profound influence on the belief system that fuels al-Qaeda, ISIS, and the Islamic Republic of Iran. Despite their disagreements, these groups share ideological underpinnings based on the writings of the late Brotherhood ideologue Sayyid Qutb and other Brotherhood writers, which shaped these entities into what they are today.

The Brotherhood has also served as a bridge for young Islamists—including bin Laden, al-Baghdadi, and al-Zawahiri—to more violent jihadist groups. Although their execution strategies may differ, at their core, all three groups maintain a shared Islamist vision of establishing a global caliphate. This core is inherently Sunni, anathema to the Shiite Islamic Republic of Iran. Nevertheless, the Brotherhood—and specifically Qutb—has had a profound impact on Iran’s development. (Source: Inside the Brotherhood, p. 146)

The Brotherhood maintains no formal ties with ISIS and al-Qaeda, and on the surface the three groups may appear dissimilar, as al-Qaeda and ISIS both advocate violent jihadism, while the Brotherhood officially seeks to transform societies from within. “The Murtadd [apostate] Brotherhood,” the March 2016 cover story in ISIS’s Dabiq magazine denouncing the Brotherhood’s supposed apostasy, is an example of ISIS’s public disapproval of the Brotherhood. The groups have, however, at times voiced support for one another. In June 2017, al-Qaeda’s Yemeni branch released a statement supporting Qatar after the country came under fire in part for supporting the Muslim Brotherhood. According to reports, many al-Qaeda leaders in Yemen were previously associated with the Brotherhood movement there, and the two groups have on occasion fought alongside one another against the Houthis. Iran, meanwhile, has supported Brotherhood-offshoot Hamas and made overtures toward the Brotherhood against mutual enemies. (Sources: Dabiq, Al Arabiya, Intercept)

Indeed, the Counter Extremism Project (CEP) has found that these groups—the Muslim Brotherhood, al-Qaeda, ISIS, and Iran—share more than deep ideological underpinnings, and their similarities far outweigh their differences. Long-term regional goals have also spurred various forms of cooperation between these groups—for example, between ISIS’s Sinai branch and the Brotherhood-affiliated Hamas, or between Iran and the Brotherhood against Saudi Arabia—as some Middle East governments rally against Islamism and Qutb-inspired jihadist groups. While these groups often differ in their public facing strategies, they are ultimately bound together by their shared ideology and their vision for an Islamic state governed by Islamic law.

While these groups often differ in their public facing strategies, they are ultimately bound together by their shared ideology and their vision for an Islamic state governed by Islamic law.

The Muslim Brotherhood and ISIS

ISIS has publicly scorned the Brotherhood as a “devastating cancer” devoted to the religion of democracy rather than Allah. Despite their operational differences, the Brotherhood has provided the platform used to indoctrinate young men into Islamism and a bridge for recruits to graduate into the more violent Islamism of ISIS. Factions within the groups have also supported each other based on shared goals, common enemies, and support for a united Islamist front. (Source: Dabiq)

Officially, the Brotherhood adheres to a non-jihadist form of Salafism and maintains a public stance of non-violence, a position adopted by the main Egyptian branch in the 1970s in exchange for permission to organize politically in Egypt. Despite this official position, the Brotherhood has nonetheless supported the violent policies of its Palestinian offshoot, Hamas. The Brotherhood has also been linked to violence in Egypt since the 2013 fall of the Brotherhood-led government there. Recruiters to violent Islamist groups also frequently use Brotherhood literature and ideology as a part of their religious indoctrination program for potential recruits, who then easily transition to overtly violent jihadist groups like al-Qaeda and ISIS. (Source: Gov.UK)

Some members of al-Qaeda and ISIS were first introduced to violent strains of Salafism through the Brotherhood before graduating to overtly jihadist Islamist groups. Chief among these is ISIS’s leader, Abu Bakr al-Baghdadi.

Abu Bakr al-Baghdadi

ISIS’s deceased self-proclaimed caliph, Abu Bakr al-Baghdadi, moved between all three Islamist organizations. Al-Baghdadi progressed from the Muslim Brotherhood’s Salafism to the violent Salafism of al-Qaeda, ultimately breaking from al-Qaeda to establish ISIS. While in graduate school at Iraq’s Saddam University for Islamic Studies, al-Baghdadi joined the Brotherhood at the behest of his paternal uncle, Ismail al-Badri. Al-Baghdadi’s older brother, Jum’a, also belonged to the Brotherhood. (Source: Brookings Institution)

Al-Baghdadi progressed from the Muslim Brotherhood’s Salafism to the violent Salafism of al-Qaeda, ultimately breaking from al-Qaeda to establish ISIS.

While the Brotherhood did not officially advocate violence, al-Baghdadi and his brother naturally gravitated toward elements of the Brotherhood who more closely aligned with a violent jihadist philosophy. Al-Baghdadi believed that the Brotherhood was controlled by “people of words, not action,” yet he easily found kindred spirits within the organization. He eventually formally left the Brotherhood to pursue a more overtly violent Islamist path. (Source: Brookings Institution)

After the 2003 U.S. invasion of Iraq, al-Baghdadi founded the militant Sunni group Jamaat Jaysh Ahl al-Sunnah wa-l-Jamaah. Al-Baghdadi eventually served time in Camp Bucca, a U.S. detention center in Iraq, where he met other prisoners who would later form the core senior leadership of ISIS. Following his release, al-Baghdadi became a top official of al-Qaeda in Iraq. In 2010, the group renamed itself the Islamic State of Iraq (ISI) and cast al-Baghdadi as its leader. In April 2013, ISI declared that the Nusra Front had pledged its allegiance to the group, a unilateral move that was contested both by Nusra Front leader Abu Mohammad al-Golani and al-Qaeda leader Ayman al-Zawahiri. ISI nonetheless changed its name to the Islamic State of Iraq and Syria (ISIS), and declared its new caliphate in June 2014. (Sources: BBC News, BBC News, New York Times, MEMRI, Al Jazeera, Agence France-Presse)

Al-Baghdadi is by no means the only extremist whose path to violent radicalism began with the Brotherhood’s extremist ideology. Foreign fighters to ISIS, such as Huseyin Mustafa Peri, illustrate the radicalizing influence the Brotherhood’s ideology continues to have in leading young men and women down the path to violent extremism.

ISIS and the Brotherhood: Common Goals Override Doctrine

While the Brotherhood and ISIS have traded accusations amid disagreements on tactics and strategy, elements within each group have found common ground and readily cooperate logistically and in other ways.


ISIS and the Brotherhood have shared a common enemy in the form of the Egyptian government since the July 2013 ouster of Egypt’s Brotherhood-centric government. Egypt outlawed the Brotherhood later in 2013, designating it a terrorist organization. Since then, the Brotherhood has been implicated in multiple terrorist attacks carried out against Egyptian forces.

For example, the Brotherhood has been blamed, in conjunction with Hamas, for a June 2015 car bomb that killed Egyptian Public Prosecutor Hisham Barakat. The following month, security forces raided a Cairo apartment in which they believed the Brotherhood was planning terrorist attacks. Nine Brotherhood members, including a former parliamentarian, died in the raid. The Brotherhood, in turn, called the incident a “turning point” and called for a country-wide revolt. (Sources: Counter Extremism Project, Associated Press, Wall Street Journal, New York Times, Guardian)

ISIS also declared its opposition to the Egyptian government and claimed responsibility for the crash of Russian flight 9268 in the Sinai, which killed 224 people on October 31, 2015. (Sources: CNN, BBC News, Independent, BBC News, Al Jazeera)

ISIS maintains an affiliate in Egypt’s Sinai Peninsula, Wilayat Sinai (Sinai Province), giving the group a foothold in Egypt and allowing it to direct attacks against the state. The terrorist group, previously known as Ansar Beit al-Maqdis, pledged allegiance to ISIS in November 2014 and changed its name to Wilayat Sinai. The group reportedly has between 1,000 and 1,500 members. Wilayat Sinai has staged increasingly bloodier attacks on the Egyptian military since July 2015. Egypt launched a major military campaign against Wilayat Sinai in 2018, killing hundreds of militants, according to the Egyptian government. Nonetheless, the group continues to carry out sporadic attacks in the country. In April 2019, Wilayat Sinai announced it would expand its attacks into the southern Sinai Peninsula, where Egypt has a stronger security presence. (Sources: CNN, BBC News, Independent, BBC News, Al Jazeera, Reuters, Mada)

In January 2016, ISIS called on the Muslim Brotherhood in Egypt to abandon its non-violent philosophy and openly take up arms against the Egyptian government.

In January 2016, ISIS called on the Muslim Brotherhood in Egypt to abandon its non-violent philosophy and openly take up arms against the Egyptian government. A video by ISIS released on January 23 urged the “Muslim brothers” in Egypt to “use the experience you gained from ousting the previous apostate regime of Hosni Mubarak” to topple “the current apostate regime of President al-Sisi.” Some Egyptian observers see clear evidence that younger Brotherhood members are increasingly turning to violence in the face of government crackdowns on their organization. They point to violent raids and former president Mohammed Morsi’s death sentence as sending the message that the group’s anti-violence stance is ineffective. ISIS supporter Abu Azzam al-Ansari may have been speaking for many when he tweeted in June 2015: “The peacefulness of the Brotherhood, on which it still insists, led its leaders to death and allowed its enemies to walk out completely innocent. Peacefulness is not accepted by beasts.” (Sources: Jerusalem Post, Al-Monitor)

ISIS has also capitalized on Egyptian violence to lure younger Egyptians to its cause. As violence mounts in Egypt, some Brotherhood members are turning to jihadist groups to exact revenge against the government and the army. A sheikh from the Sawarka tribe in Egypt’s Sinai Peninsula claims that the ongoing violence is transforming younger Brotherhood members living in the Sinai “into human resources used by IS for its operations in Sinai.” The sheikh believes the fighting will spawn new ISIS cells in Egypt and states that, “One cannot separate the Brotherhood from IS.” (Source: Al-Monitor)

According to former Brotherhood activist Mustafa el-Nemr, more than 100,000 families have reason to seek retaliation against Egyptian President Abdel Fattah el-Sisi. El-Nemr now lives in Turkey after serving a prison sentence in Egypt. El-Nemr observed that younger Brotherhood members are stepping into leadership roles in Egypt. These younger members believe in a “defensive violence,” according to Shadi Hamid of the Brookings Institution. As the most prominent jihadist group operating in the Sinai, ISIS’s Wilayat Sinai is believed to be well-stationed to take advantage of young Egyptians seeking revenge against the Egyptian government. (Source: Time)

Hamas and Wilayat Sinai

The Sinai Peninsula may offer the best example of direct cooperation between the Muslim Brotherhood and ISIS. After the fall of Egypt’s Brotherhood-led government in 2013, Palestinian Brotherhood offshoot Hamas and Wilayat Sinai increasingly cooperated against the Egyptian government, which has ramped up military operations against both groups since 2013.

Egypt has flooded dozens of Hamas’s smuggling tunnels beneath the Gaza-Egypt border, and Egyptian courts have debated declaring Hamas a terrorist organization. Following meetings between the Hamas leadership and the Egyptian government in March 2016, Hamas denied any links to the Brotherhood. (Sources: Al Jazeera, Reuters, Haaretz)

Despite Hamas’s public efforts to repair its relations with Egypt, the group’s military wing, the Izz ad-Din al-Qassam Brigades, boosted its cross-border cooperation with Wilayat Sinai as a result of the pressure they have increasingly sensed from Egypt. Wilayat Sinai leaders have reportedly met with Hamas to discuss military coordination. Hamas has purportedly used its fledgling drone program to spy on Egyptian military positions on behalf of Wilayat Sinai. Hamas has also allegedly given Wilayat Sinai access to its network of underground tunnels beneath the Gaza-Egypt border. According to a report by Ynet News, Hamas paid Wilayat Sinai tens of thousands of dollars a month through 2015 to smuggle weapons from the Sinai into Gaza, while Hamas has also smuggled weapons into the Sinai. Wilayat Sinai fighters have also reportedly received medical treatment in Gaza. (Sources: Times of Israel, Algemeiner, Ynet News)

Relations between Hamas and Wilayat Sinai began to unravel in 2017. Hamas agreed to boost its security presence along the Sinai-Gaza border as part of a reconciliation agreement with the Egyptian government. That June, Hamas began constructing a buffer zone along the border to decrease smuggling in exchange for Egypt loosening its closure of its border with Gaza and providing electricity to the territory. In August, an ISIS suicide bomber killed a Hamas border guard in the Gaza Strip in the first suicide bombing to target Hamas. In January 2018, Wilayat Sinai released a video in which the group executed one of its members accused of smuggling weapons to Hamas. A Gaza native and ISIS cleric in the Sinai identified as Abu Kazem al-Maqdisi called on ISIS’s followers to attack Hamas over its failures to prevent U.S. recognition of Jerusalem as Israel’s capital. (Sources: United Press International, Times of Israel, Times of Israel)


Brotherhood members in Libya have reportedly joined ISIS and al-Qaeda training camps. According to a January 2016 news report, young members of the Brotherhood receive between $150 and $250 per day to take part in the Libyan training camps. (Source: Al-Bawaba)

The Muslim Brotherhood and Al-Qaeda

The Brotherhood’s role as a bridge to jihadist organizations is perhaps most visible in the group’s ties to al-Qaeda. The United States sanctioned Sheikh Abd al-Majeed al-Zindani in 2004, for example, for a “long history of working with bin Laden, serving as one of his spiritual leaders.” Al-Zindani also led the Brotherhood’s al-Islah political party in Yemen. (Source: U.S. Congress, U.S. Department of the Treasury)

U.S. authorities arrested Mohammad Jamal Khalifa in 1994 in connection with the 1993 World Trade Center bombing. He was also a senior Brotherhood leader, according to the U.S. government. He later operated a charity in the Philippines that allegedly funneled money to the Abu Sayyaf Group and also laundered money for bin Laden. He was killed in 2007. (Source: U.S. Congress)

The Brotherhood also supported the 1988 creation of Bank Al Taqwa in the Bahamas. The U.S. government revealed that the bank was a shell company that supported terrorist groups such as Hamas, the Islamic Salvation Front, and al-Qaeda. According to the U.S. Treasury, the bank provided “a clandestine line of credit” to a close associate of bin Laden’s. The government accused the bank’s director, Youssef Nada, of providing financial assistance to al-Qaeda and bin Laden. (Source: U.S. Department of the Treasury)

Several of al-Qaeda’s most famous leaders have also passed through the Brotherhood.

Mohammed Badie, the Brotherhood’s supreme spiritual guide, gave a 2010 sermon that paralleled the 1996 al-Qaeda declaration targeting the West. Specifically, Badie declared that resistance through “jihad and sacrifice and by raising a jihadi generation that pursues death just as the enemies pursue life” is the “only solution against the Zio-American arrogance and tyranny.” He further declared that the United States “is now experiencing the beginning of its end, and is heading towards its demise.” An Egyptian court sentenced Badie to death in 2015 for planning attacks against Egypt, though the sentence was later overturned. (Sources: U.S. Congress, BBC News, Business Standard)

These examples led to the November 2015 introduction of the Muslim Brotherhood Terrorist Designation Act in both Houses of Congress. The bill called for the United States to designate the Brotherhood as a terrorist organization and listed former Brotherhood members who went on to join al-Qaeda and were later designated as terrorists by the United States. (Source: U.S. Congress)

Several of al-Qaeda’s most famous leaders have also passed through the Brotherhood.

Osama bin Laden

The most famous former Brotherhood member to join al-Qaeda is the group’s co-founder, Osama bin Laden. Bin Laden belonged to the Brotherhood’s chapter in the Arabian Peninsula, according to al-Qaeda co-founder Ayman al-Zawahiri.

In an April 2011 message sent just a week before his death, bin Laden said groups like the Brotherhood call only for “half solutions,” but there are Salafist streams within the group that recognizes the truth. Bin Laden predicted that the Brotherhood would align itself with the violent jihadism of al-Qaeda, saying “the return of the Brotherhood and those like them to the true Islam is a matter of time.” (Source: Long War Journal)

Following bin Laden’s death in 2011, the Brotherhood in Egypt released a statement referring to bin Laden by the honorific “sheikh.” The Brotherhood also praised the “resistance” in Afghanistan and Iraq, crediting bin Laden. (Sources: Atlantic, Long War Journal)

Ayman al-Zawahiri

Ayman al-Zawahiri co-founded al-Qaeda with Osama bin Laden in 1988. Years earlier, he had joined the then-outlawed Brotherhood as a teenager in Egypt, for which he was arrested at age 15. Al-Zawahiri went on to join the Egyptian Islamic Jihad (EIJ) in 1973, and he was arrested with other EIJ members in 1981 for the assassination of President Anwar al-Sadat. Al-Zawahiri is a former leader of the EIJ, which merged with al-Qaeda in 2001. (Sources: U.S. Department of State, BBC News)

Zawahiri has condemned Egypt’s crackdown on the Muslim Brotherhood. The Egyptian newspaper El-Watan has reported conversations between Egypt’s former president Mohammed Morsi and al-Zawahiri’s brother, Muhammad al-Zawahiri. According to these conversations, while president, Morsi allegedly colluded with al-Zawahiri to release terrorists from Egyptian prisons in order to garner support for the Brotherhood. (Sources: Daily News Egypt, Jerusalem Post)

Khalid Sheikh Mohammed

The Brotherhood had a profound influence on al-Qaeda operative and 9/11 mastermind Khalid Sheikh Mohammed, according to a 2011 profile in the New Yorker.

Mohammed’s family moved to Kuwait from Pakistan in the 1950s. He was born in Kuwait in 1965. After his father died four years later, Mohammed’s brothers took responsibility for his education. The Brotherhood was technically illegal in Kuwait, but the government allowed it to operate in order to maintain control. Mohammed watched as his older brother Zahed became a Brotherhood student leader at Kuwait University. Following his brother, Mohammed began attending Brotherhood-run camps at the age of 16. There, he learned about the group’s ideology and one of its most famous ideologues, Sayyid Qutb. He reportedly became enamored with Qutb’s anti-Western and jihadist teachings.

After high school, Mohammed in 1984 went on to study engineering in the United States. He reportedly developed a dislike of Americans while studying in North Carolina, considering them racist. According to one of Mohammed’s teachers in Kuwait, he returned from the United States in 1986 convinced that America hated Arabs because of the country’s relationship with Israel.

Soon after he returned to Kuwait, Mohammed followed his brothers to Pakistan where they were working on war relief efforts. It was in Peshawar, Pakistan, where Mohammed came into contact with Osama bin Laden and Ayman al-Zawahiri, the future leaders of al-Qaeda. Their paths diverged from that point, but Mohammed and bin Laden would renew their relationship in 1996, three years after Mohammed’s nephew Ramzi Yousef masterminded the first attack on the World Trade Center.

Yousef had inspired Mohammed to take an active role in planning attacks against the United States. When Mohammed and bin Laden met again in 1996, they began laying the groundwork for the 9/11 attacks.

(Sources: New Yorker, Long War Journal, 9/11 Commission Report, pp. 145-150)

The Brotherhood and the Nusra Front

Al-Qaeda’s former affiliate in Syria, the Nusra Front, is a rebel group dedicated to replacing President Bashar al-Assad’s government with an Islamist regime. The Nusra Front’s leader, Abu Muhammad al-Golani, has been critical of the Brotherhood for deviating from traditional Islamic teachings, yet the Nusra Front has been documented using materials from the Brotherhood in the group’s religious indoctrination program. (Source: National)

In 2014, the Syrian Brotherhood elected Mohammad Hekmat Walid to a four-year term as the group’s leader. During a May 2015 interview with Al Jazeera, Walid refused to publicly condemn the Nusra Front or ISIS as terrorist groups. He instead called al-Assad and his regime “the biggest terrorists” in Syria. Walid also condemned the counterterrorism work of the international coalition in Syria as selective, as well as “suspicious and confusing.” (Source: Al Jazeera)

The Brotherhood had defended the Nusra Front in 2012 after the United States labeled the group a terrorist organization. Farouk Tayfour, then the Syrian Brotherhood’s deputy leader, called the designation “very wrong and too hasty” given what he called the “grey atmosphere” at the time in Syria. According to Tayfour, the Syrian people view the Nusra Front as a reliable defense against “the regular army and Assad’s gangs.” (Source: Reuters)

In 2016, the Nusra Front formally changed its name to Jabhat Fatah al-Sham and renounced any formal ties to al-Qaeda. The Brotherhood’s Syria faction praised the decision as a step toward making the Syrian revolution “truly local.” The following year, Golani praised the shared ideology of al-Qaeda and the Brotherhood. While they may differ in their tactics, both groups derive their ideologies from the same sources, Golani told Al Jazeera. (Sources: Ikhwanweb, Arab News)

The Muslim Brotherhood and Iran

The Sunni Muslim Brotherhood and the Shiite Islamic Republic of Iran do not seem like natural allies at first glance. Nor do they maintain formal relations. While the Brotherhood and the Iranian government do not have organizational links, they do have ideological ties. The Brotherhood was influential on the creation of the Islamic Republic and its leaders.

In 1946, Iranian theology student Mojtaba Mir-Lohi, a.k.a. Navvab Safavi, created the Fedayeen-e-Islam, “Organization of Islamic Society.” The group sought to purify Iran by eliminating what it considered impure individuals. Fedayeen-e-Islam was reportedly modeled on Nizam al-Khaas (“Secret Apparatus”), the Brotherhood’s underground armed faction in Egypt responsible for a number of assassinations. In the 1950s, Safavi met with Brotherhood ideologue Sayyid Qutb, who invited Safavi to visit Egypt and Jordan. There, Safavi met other leaders of the Brotherhood. Safavi would later introduce Ruhollah Khomeini to the Muslim Brotherhood. Safavi was executed in 1956, but he had successfully influenced the future revolution before his death. The Brotherhood-inspired Fedayeen-e-Islam later supported Khomeini’s vision of an Islamic republic in Iran during the 1970s, and its members became foot soldiers for the government after the 1979 Iranian Revolution. (Sources: Jewish Chronicle, TRAC, Al Arabiya, Al Jazeera, Al Jazeera)

Iran’s current supreme leader, Ali Khamenei, heard Safavi speak at his school as a teenager. Khamenei credited Safavi with engaging him in politics as he began supporting the ideology of Safavi’s Fadayan-e Islam movement. Khamenei went on to translate two books of Qutb’s books into Persian. (Sources: Comparative Strategy, Journal of Islamic and Muslim Studies,, European Eye on Radicalization)

Despite divisions between Shiites and the Sunni Brotherhood, the Brotherhood supported the idea of Khomeini’s 1979 Iranian Revolution as a realization of their goal of an Islamic state. Ahead of Khomeini’s return to Iran, the Brotherhood sent representatives from its global chapters to Paris to congratulate him on successfully popularizing the revolution. In 1982, Brotherhood leader Umar Telmesani said the Brotherhood supported Khomeini politically, though Sunnis and Shiites remained religiously divided. Khomeini’s government made a handful of overtures toward the Brotherhood. Khomeini’s Iran issued a postage stamp in 1984 commemorating Qutb’s 1966 execution. In 1988, Khomeini’s government unilaterally released Egyptian prisoners of war who had fought alongside Iraq in the Iran-Iraq War at the request of Brotherhood leader Shaikh Muhammad Ghazzali. (Sources: Al Arabiya, TRAC,, Washington Institute for Near East Policy, European Eye on Radicalization)

Both the Brotherhood and Khomeini embraced the centrality of Islam to politics and governance. And while the Brotherhood and Iran remain divided along sectarian lines, the Brotherhood early on recognized Khomeini’s vision as a realization of the goal they had long promoted. Early Brotherhood ideologue Abul Ala Maududi declared in 1939 that “Islam is not merely a religious creed or compound…but a comprehensive system which envisages to annihilate all tyrannical and evil systems in the world.” Khomeini’s concept of vilayat-e-faqih (“guardianship of the Islamic jurist”), based on a ninth-century Shiite philosophy, introduced the concept of an Islamic jurist with final authority over Iran’s political and religious spheres in order to ensure compliance with religious law. (Sources: Al-Islam, Hudson Institute, Brookings Institution, Dawn, Muhammadanism)

Shared Ideologies

Al-Qaeda, ISIS, and the Iranian regime were inspired by the Muslim Brotherhood’s core ideology. ISIS sprung from al-Qaeda in Iraq and al-Qaeda’s founders were students of early Brotherhood ideologues, such as theoretician Sayyid Qutb. As a result, violent extremist groups such as ISIS serve as an extension of core Brotherhood ideology, according to Egyptian Minister of Religious Endowments Mohamed Mokhtar Gomaa. Jordanian analyst Fehmi Jadaane also believes that the ideologies of ISIS and the Brotherhood are fundamentally one and the same. While Iran’s revolutionaries adopted different tactics than the Brotherhood or al-Qaeda, the Brotherhood’s ideological influence is present as well among the founders of the Islamic revolution. (Sources: Seventh Day, MEMRI, Jerusalem Post, Telegraph)

Sayyid Qutb

Sayyid Qutb (1906-1966) was a leading theoretician of the Muslim Brotherhood whose works inspired a range of violent Islamists, including Osama bin Laden and Ayman al-Zawahiri. Western critics have labeled Qutb the father of modern Islamic fundamentalism. According to the 9/11 Commission Report, Qutb was a particularly “strong intellectual influence” on bin Laden. In his book Knights under the Prophet’s Banner, al-Qaeda leader Ayman al-Zawahiri praised Qutb for beginning the jihadist movement. In Iran, Qutb was widely read by those who would go on to build and support Khomeini’s revolution. Writing in the Journal of Islamic and Muslim Studies, Yusuf Unal called Qutb an “influential figure” among Iranian revolutionaries. Qutb’s writings played “an instrumental role in shaping the discourse of Islamism in pre-revolutionary Iran.” (Sources: New Yorker, Guardian, 9/11 Commission Report, p. 56, Al Arabiya, Journal of Islamic and Muslim Studies)

Qutb’s writings on Islamism are among the most popular in the Muslim world. Qutb wrote that Islam was “a revolt against any human situation where sovereignty, or indeed Godhead, is given to human beings.” Qutb believed Islam meant restoring God’s authority over man. He rejected Western secularism and believed the modern state of Egypt to be un-Islamic. While studying in America between 1948 and 1950, Qutb was repulsed by what he perceived to be American indecency. He described churches as “entertainment centers and sexual playgrounds.” He viewed the entirety of American culture as corrupt, unjust, racist, materialistic, and morally vacant. He also detested America’s recognition of the new country of Israel. (Sources: Guardian, Jamestown Foundation, 9/11 Commission Report, p. 51)

Qutb’s writings expanded the concept of jahiliyya, used to describe the barbaric, ignorant state before the Prophet Muhammad’s revelation. Qutb believed that the world was in a state of new jahiliyya, and that Muslims everywhere were living as blindly and ignorantly as civilization had in the time before Mohammad. He argued that Muslims must return to living in a state of “pure Islam,” which they could accomplish only by waging violent jihad against the non-believers. His two most famous works, Fi Zilal al-Qur’an (In the Shade of the Quran) and Ma’alim fi’l-Tariq (Milestones),were both written while in prison. Sheikh Omar Abdel Rahman, also known as the “Blind Sheikh,” used Milestones as inspiration for his preaching. Rahman is serving a life sentence in the United States on terrorism charges. (Sources: Guardian, Jamestown Foundation, New York Times, 9/11 Commission Report, pp. 51, 72)

Western critics have labeled Qutb the father of modern Islamic fundamentalism.

Qutb believed that humanity had a choice between jahiliyya and Islam. He also believed there could be no middle ground between the two—that Islam represented God while jahiliyya represented Satan. Years later, bin Laden would look to Qutb’s views in order to justify al-Qaeda’s violent attacks as a defense against the enemies of Islam, chief among them, the United States. (Source: 9/11 Commission Report, p. 51)

Qutb was hanged for extremist rhetoric and the attempted assassination of Egyptian President Gemal Abdel Nasser on August 29, 1966. His teachings inspired Brotherhood members who went on to form groups such as al-Gama’a al-Islamiyya and the Egyptian Islamic Jihad (EIJ) in the 1970s and 1980s. The EIJ merged with al-Qaeda in 2001.

Qutb’s influence can be seen outside of the Brotherhood as well. According to a founding member of al-Gama’a al-Islamiyya, “Qutb has influenced all those interested in jihad throughout the Islamic world.” Al-Zawahiri said that Qutb’s “call for loyalty to God’s oneness and to acknowledge God’s sole authority and sovereignty was the spark that ignited the Islamic revolution against the enemies of Islam at home and abroad. The bloody chapters of this revolution continue to unfold day after day.” (Sources: New Yorker, Foreign Affairs, Council on Foreign Relations, BBC News, Gov.UK, His Own Words: A Translation of the Writings of Dr. Ayman al Zawahiri, p. 48)

“Qutb has influenced all those interested in jihad throughout the Islamic world.”

The Caliphate

Central to the Islamist ideology is the concept of a caliphate, a state ruled by Islamic law headed by an individual anointed as the caliph (literally successor), who is believed to be the descendant of the Islamic prophet Muhammad. The last Islamic caliphate dissolved in 1924 with the dissolution of the Ottoman Empire and the emergence of the various nation-states that today comprise the modern Middle East. Muslim Brotherhood founder Hassan al-Bana rejected the nation-states created after the fall of the Ottoman Empire. He instead advocated pan-Arab nationalism and the creation of a single Islamic caliphate.

While the Brotherhood, al-Qaeda, and ISIS each believe in a caliphate, they differ in their approaches to accomplishing this shared vision. (Sources: Time, Ikhwanweb, Ikhwanweb, Al Jazeera)

The Muslim Brotherhood tries to “build a popular base that believes in the Islamic system and is aware of its main ideas.” The Brotherhood’s primary tools to effect change are dawa (proselytization) and political participation. In Egypt’s 2012 elections, for example, the Brotherhood capitalized on goodwill built from decades of providing social services to win Egypt’s presidency. (Sources: Ikhwanweb, Ikhwanweb, Middle East Political Science, Al Jazeera)

Al-Qaeda believes a global Islamic caliphate will help Muslims return to the Islamic practices of the first generation of Muslim leaders. Al-Qaeda challenges what it considers the West’s global hegemony through “defensive jihad,” to protect Muslim lands from the “new crusade led by America against the Islamic nations….” Osama bin Laden’s 1996 fatwa outlined al-Qaeda’s goals of uniting Muslims under sharia, removing the U.S. presence from Islamic holy lands, and righting injustices by the “Zionist-Crusader alliance.” (Sources: Congressional Research Service, PBS Newshour)

In 2005, media sources revealed al-Qaeda’s multi-phase 20-year plan to achieve this goal. The plan began with the “awakening stage” between 2000 and 2003, which called for a massive attack on New York to push the United States to react. Next would come a stage of direct combat between 2003 and 2006, followed by increased al-Qaeda activity in the Middle East and efforts to topple Arab regimes. Al-Qaeda would then, according to this plan, declare a caliphate between 2013 and 2016. (Sources: Long War Journal, Al-Akhbar English)

While al-Qaeda succeeded in some of these stages—such as the 9/11 attacks and engaging U.S. forces in Afghanistan—ISIS has usurped al-Qaeda’s timeframe. Al-Qaeda under bin Laden perceived the creation of an Islamic state as a long-term goal secondary to the immediate goal of toppling America. (Sources: Long War Journal, Al-Akhbar English)

Documents recovered from bin Laden’s compound in Pakistan show that he believed striking at the United States was more important than forming an Islamic caliphate. The difficulties of daily governance and maintaining popular support for a caliphate concerned bin Laden. In one letter, bin Laden wrote that al-Qaeda must ensure it can control a state before creating one. To that end, he believed al-Qaeda must first defeat its chief enemy: America. “Even though we were able to militarily and economically exhaust and weaken our greatest enemy before and after the eleventh, the enemy continues to possess the ability to topple any state we establish,” he wrote. (Sources: Bloomberg News, CNN, Office of the Director of National Intelligence)

Al-Qaeda has also condemned ISIS’s declaration of a caliphate “without consulting the Muslims.” Al-Zawahiri lashed out at ISIS for not coordinating its caliphate with other jihadist groups through sharia courts, which he has referred to as the “prophetic method.” (Sources: ABC News, Long War Journal)

ISIS announced its resurrection of the caliphate in June 2014, declaring that without the realization of a caliphate “all power is simply worldly kingship, domination and governance, accompanied by destruction, corruption, injustice, coercion and fear, and the degradation and decline of humans to the level of animals.” Though ISIS lost the last of its territorial hold in Iraq and Syria by March 2019, the group has established what it calls provinces outside of Syria and Iraq as part of its goal to expand its caliphate. (Sources: Foreign Affairs, International Business Times, CNN, Dabiq)

For Iran, the idea of an Islamic state is not theoretical. Khomeini first envisioned an Islamic state in Iran as early as 1941 in his book, Unveiling the Mysteries. Only a state “directed and organized according to the divine law” would be acceptable to God, he wrote. Unlike in al-Qaeda’s and ISIS’s envisioned states, Khomeini’s Islamic republic did not necessarily have to be run by the clergy. Still, he wrote, clerical supervision would be necessary to ensure compliance with religious law. (Source: New York Times)

Here again Khomeini drew influence from the Brotherhood. The clerical oversight Khomeini envisioned echoed Qutb’s writings that people should not be allowed to make choices in contravention of the divine. “God has formed the Islamic Republic,” Khomeini wrote in Unveiling the Mysteries. So while the Brotherhood largely promoted a slow and strategic methodology to achieve the caliphate through the ballot box in existing states, Khomeini conditioned his followers to act decisively to bring out an Islamic state within Iran through revolution. As Khomeini solidified his vision in the 1960s, he developed mechanisms for clerical oversight of the government and made religious belief a core principle of every facet of his then-theoretical Islamic state. Khomeini consolidated clerical control over the fledgling Iranian government in the aftermath of the revolution. (Sources: New York Times, Inside the Brotherhood, p. 173-174, Islamic Parliamentary Research Center)

Potential for Alliances

In January 2016, the London-based Arab newspaper Asharq al Awsat reported that ISIS, al-Qaeda, and the Muslim Brotherhood were discussing the formation of a joint shura (leadership) council in Libya, according to leaked document obtained by the newspaper. The paper reported that the discussions of an alliance are because the groups want to send a message of joint opposition from Libya’s Islamists to the Libyan unity government. Brotherhood members in Libya have reportedly received daily salaries for joining ISIS and al-Qaeda training camps. (Sources: Asharq al Awsat)

In September 2015, Ayman al-Zawahiri issued a statement that “if there is fighting between the Crusaders, the Safavids, and the secularists, with any group from the Muslims and the mujahideen, including the group of Abu Bakr al-Baghdadi and those with him, then our only choice is to stand with the Muslim mujahideen….”

In a March 2016 article for Foreign Affairs, author Bruce Hoffman posited that al-Qaeda and ISIS could be headed toward a merger due to common ideologies and a shared conviction that Muslims should unite when threatened. In September 2015, Ayman al-Zawahiri issued a statement that “if there is fighting between the Crusaders, the Safavids, and the secularists, with any group from the Muslims and the mujahideen, including the group of Abu Bakr al-Baghdadi and those with him, then our only choice is to stand with the Muslim mujahideen….” (Sources: Foreign Affairs, CNN)

Al-Qaeda has also reached out to the Brotherhood. Leaders of both groups reportedly held meetings in October 2013 in Jordan. They purportedly discussed plans to begin moving Syrian and Iraqi al-Qaeda fighters into Egypt to oppose the new military-led government, which had a few months earlier ousted the Brotherhood from political power. Those meetings have not resulted in official ties between the two groups, but al-Qaeda leader Ayman al-Zawahiri—who has regularly praised Brotherhood ideologue Sayyid Qutb—has come to the Brotherhood’s defense on the international stage. In 2018, Saudi Crown Prince Mohammed bin Salman pledged on U.S. news show 60 Minutes that Saudi Arabia would eliminate any last vestiges of Brotherhood ideology from its schools. Zawahiri released an audio recording accusing Saudi Arabia and the United States of working together to rewrite Islamic history. He further called for all Muslims to unite and focus their energies on fighting the United States. (Source: Jerusalem Post, The National)

In June 2017, Saudi Arabia, Bahrain, the United Arab Emirates, and Egypt severed relations with Qatar, citing Qatari support for the Brotherhood and other terrorist groups. The countries also designated several Brotherhood-linked individuals based in Qatar, including Brotherhood ideologue Yusuf al-Qaradawi. In response, al-Qaeda issued a video called “the mask has fallen,” condemning the actions against Qatar and the Brotherhood. The al-Qaeda newspaper Al-Masra blamed the diplomatic break on Arab annoyance with Qatari support for the Brotherhood and the country’s involvement in Yemen. AQAP’s Khalid Batarfi reportedly called the sanctions a “war against Islam and Muslims” by “tyrants.” (Sources: Al Arabiya,

Egyptian Minister of Religious Endowments Mohamed Mokhtar Gomaa believes Islam should be kept separate from political affairs. Gomaa has called the Brotherhood’s year in power “the worst” in Egypt’s modern history. He warned in 2014 that ISIS and the Brotherhood were heading toward a formal alliance, and predicted that Brotherhood leaders recently released from Egyptian prisons would form violent groups that would “incite from Qatar, conspire from Libya, mobilise the international organisation [of the Muslim Brotherhood] in Turkey and ally with the Islamic State [ISIS].” (Sources: Seventh Day, Arab Daily News, Daily News Egypt)

Given the intensity of disagreement between the Sunni and Shiite philosophies, it is unlikely that Iran and the Brotherhood would develop any formal cooperation. Nonetheless, Brotherhood leaders have demonstrated admiration for the core idea of the Iranian revolution. In January 1982, Brotherhood leader Umar Telmesani elaborated to Egyptian media though large doctrinal gaps remained between Sunnis and Shiites, the Brotherhood had supported Khomeini “politically, because an oppressed people had managed to get rid of an oppressive ruler and to regain their freedom….”" In January 2009, Brotherhood leader Muhammad Mahdi Akef told the Mehr News Agency the Brotherhood “supports the ideas and thoughts of the founder of Islamic Republic.” Akef praised Khomeini’s “continuation of the Muslim Brotherhood’s attitude toward fighting occupation.” (Source: Washington Institute for Near East Policy)

That shared attitude resulted in Iran’s largest operational link to the Brotherhood: Iranian support for the Brotherhood offshoot Hamas. Iran has provided the Gaza-based terror group with weapons, training, and money. Though Hamas is a primarily Sunni organization, Iran’s support transcended the Shiite-Sunni divide based on a common enemy in Israel. Iran provided financial and military support during Hamas’s suicide bombing campaign during the Second Intifada and for Hamas’s arsenal of rockets. Following Hamas’s electoral victory in the January 2006 Palestinian elections, Iran equipped Hamas with an estimated $23 million a month in financial and military aid, including for governing expenses. In August 2017, Hamas’s political leader in Gaza, Yahya Sinwar, called Iran the “largest backer financially and militarily” of Hamas. Calling Iranian military support to Hamas “strategic,” Sinwar told reporters that Iran is aiding Hamas in building its “military strength in order to liberate Palestine.” Hamas may have since renounced its ties to the Brotherhood but those ties were never a hindrance to Iranian support of the group. (Sources: United Against Nuclear Iran, Telegraph, BBC News, Times of Israel)

Despite their ideological divide, Iran and the Brotherhood have come close to uniting. Egypt and Iran renewed diplomatic contacts during the 2012-2013 president of the Brotherhood’s Mohammed Morsi. Morsi visited Iran in 2012, marking the first state visit by an Egyptian leader since the two countries broke off relations following Egypt’s 1979 peace treaty with Israel. Mahmoud Ahmadinejad then became the first Iranian head of state to visit Egypt in early 2013. Yet when Morsi was overthrown later that year, Iran’s ayatollahs blamed his subservience to the United States and Israel. (Sources: Washington Post, Radio Free Europe/Radio Liberty)

In 2014, representatives of the Brotherhood and Iran’s Quds Force, the foreign expeditionary arm of the Islamic Revolutionary Guard Corps, met in Turkey to discuss an alliance against Saudi Arabia. According to a Brotherhood source quoted in a leaked Iranian Ministry of Intelligence and Security (MOIS) cable, the two shared a hatred of Saudi Arabia and discussed uniting against their common enemy in Yemen. The talks ultimately collapsed over disagreements of global tactics and strategy. The Turkey meeting may have ended in failure but it demonstrated that there is a desire—if not a strong will—for the Brotherhood and Iran to reconcile. (Sources: Intercept, New York Times)


In 1978, Ruhollah Khomeini established the Islamic Republic of Iran and realized a long-held goal of the Brotherhood with the creation of an Islamic state. Notwithstanding Khomeini’s successful transformation of Iran through revolution, the Muslim Brotherhood largely remains committed to realizing its goal through a more peaceful transition by transforming existing governments and societies from within. It aims to garner social power and widespread support in order to ultimately establish political dominance. Al-Qaeda believes the immediate goal is to defeat the primary enemy of Islam: America, after which a caliphate can be created. To do this, it needs physical power to confront the United States and religious power—or authority—to inspire others to its cause. ISIS requires physical, political, and religious power—or authority—to maintain, expand, and justify its territory and attract new followers. Iran has amassed all three, enabling it, unlike ISIS, to maintain its oppressive religious state through fear and military strength all under religious oversight.

The Brotherhood, al-Qaeda, ISIS, and Iran can at times be nominal rivals, based on tactical, strategic, and ideological disagreements. But through the sharing of a core ideology, these groups remain fundamentally tied to one another. Frequent informal partnerships and cooperation could easily evolve into high-level coordination—given their deeply held beliefs and shared goals. Iran and the Brotherhood have already attempted—and failed—to unite against mutual enemies. And while the Brotherhood and Iran are likely to remain apart because of ideological differences, the impact of the Brotherhood on modern Iran’s development cannot be ignored. That common core belief in the supremacy of Islam and the necessity of a theocratic state ruled by Islam forms the core of all of these entities.

Related Content

Daily Dose

Extremists: Their Words. Their Actions.

In Their Own Words:

We reiterate once again that the brigades will directly target US bases across the region in case the US enemy commits a folly and decides to strike our resistance fighters and their camps [in Iraq].

Abu Ali al-Askari, Kata’ib Hezbollah (KH) Security Official Mar. 2023
View Archive