As early as the mid-1950s, Elijah Muhammad began having sexual liaisons with his personal secretaries and other NOI women. For years, Muhammad's chief lieutenants at Chicago's Temple No. 2 were able to contain the rumors, sometimes through fear and intimidation. Scholar Karl Evanzz estimates that the total number of children born from Elijah Muhammad's adulterous affairs was between thirteen to twenty-one. In the Spike Lee film, Malcolm is presented as being completely and utterly in the dark about his mentor's infidelities for years. The evidence suggests otherwise, because although Malcolm X had become a minister, he had retained all of his critical ethnographic skills of participant observation that are central to survival in the ghetto.

Although the NOI was unquestionably a patriarchal and deeply conservative Islamic sect, the role and significance of women in all aspects of the organization's works should not be underestimated. Clara Muhammad, Elijah Muhammad's wife, was said to have first introduced her husband to the teachings of the sect's founder, W.D. Fard. Clara Muhammad was largely responsible for establishing the University of Islam in Detroit in 1943. When Elijah Muhammad was incarcerated during World War II, she alone held the small formation together, communicating her husband's directives to all ministers and officials. Within the NOI, young women were instructed in domestic skills through the Muslim Girls Training (MGT) and in general education courses, termed General Civilization Classes (GCC). Many women who joined the NOI did so for the same reasons that Malcolm had done. Some had been incarcerated in prison, unemployed, or had earned their livelihood through prostitution and drugs. The NOI gave them a sense of hope, self-respect and a restoration of dignity. The "protections" of black patriarchy provided a secure but clearly subordinate status for black women.

Evanzz suggests that Malcolm X had, prior to his marriage to Betty Shabazz, been attracted to another woman in Temple No. 7, Evelyn X. Supposedly, when Evelyn X was informed about Malcolm's unexpected marriage to Betty Shabazz, she left the mosque in tears. Elijah Muhammad then became sexually involved with her. As Evelyn X Williams later informed the press, "He told us that under the teaching of the Holy Koran, we were not committing adultery and that we were his wives." By 1962, when Clara Muhammad became fully aware of her husband's eight children born out of wedlock to different women, she painfully withdrew from an active role in the organization for several years. When media sources learned about Elijah Muhammad's sexual affairs, the women were censured and described as "prostitutes" in Muhammad Speaks. In July 1964, after his break with the NOI, Malcolm X persuaded Evelyn X Williams and another woman sexually victimized by Elijah Muhammad to file paternity suits. Both women suffered extreme harassment, and were forced to move when explosions occurred next to their shared living quarters.

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