Objective: To investigate self-report of heterosexual anal intercourse among male sex workers who sell sex to men, and to identify the socio-demographic characteristics associated with practice of the behavior. Design: Two cross-sectional surveys of male sex workers who sell sex to men in Mombasa, Kenya. Methods: Male sex workers selling sex to men were invited to participate in surveys undertaken in 2006 and 2008. A structured questionnaire administered by trained interviewers was used to collect information on socio-demographic characteristics, sexual behaviors, HIV and STI knowledge, and health service usage. Data were analyzed through descriptive and inferential statistics. Bivariate logistic regression, after controlling for year of survey, was used to identify socio-demographic characteristics associated with heterosexual anal intercourse. Results: From a sample of 867 male sex workers, 297 men had sex with a woman during the previous 30 days - of whom 45% did so with a female client and 86% with a non-paying female partner. Within these groups, 66% and 43% of male sex workers had anal intercourse with a female client and non-paying partner respectively. Factors associated with reporting recent heterosexual anal intercourse in bivariate logistic regression after controlling for year of survey participation were being Muslim, ever or currently married, living with wife only, living with a female partner only, living with more than one sexual partner, self-identifying as basha/king/bisexual, having one's own children, and lower education. Conclusions: We found unexpectedly high levels of self-reported anal sex with women by male sex workers, including selling sex to female clients as well as with their own partners. Further investigation among women in Mombasa is needed to understand heterosexual anal sex practices, and how HIV programming may respond.