This study analyzes the human rights issues affecting Muslim minorities in Kenya after 9/11, with special reference to Mombasa City. The study is based on both primary and secondary sources, content analysis of several documents and in-depth interview of11 knowledgeable persons selected through snowball method. Among the interviewees were Muslim community leaders, defense lawyers, and human rights activists, representatives of human rights organizations, Muslim youth activists and victims. The study focuses on the various forms of human rights violations suffered by Muslims in Kenya and the factors which account for these transgressions. Its framework relates human rights violations (HRV) to the internal and external factors contributing to human rights violations against Muslim minorities in Kenya. The research identifies a number of pertinent indicators of human rights violations faced by them, such as cases of arbitrary arrests and detentions, extra judicial killings, illegal extradition outside Kenyan jurisdiction, forceful disappearances and torture. In addition, the study identifies the following indicators of the internal factors facilitating human rights violations: the ab