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Non-occupational post-exposure prophylaxis (NPEP) has been recommended to prevent HIV acquisition for nearly 20 years. However, limited behavioral and clinical outcome data exist after men who have sex with men (MSM) present for NPEP. We reviewed the electronic medical records of HIV-uninfected adults who presented for NPEP at a large community health center in Boston between July, 1997 and August, 2013. Data from 894 patients were analyzed, 88.1% of whom were MSM. Consensual unprotected sex was the most common reason for NPEP visits among MSM (64.2%), followed by condom failure (30.6%). The HIV serostatus of the partner was unknown for 64.4% of the MSM, positive with unknown treatment status for 18.1%, positive and not on treatment for 4.1%, and positive and on treatment for 13.4%. Thirty-nine patients subsequently became HIV-infected (4.4%), all of whom were MSM. The MSM-specific HIV incidence after NPEP use was 2.2 cases per 100 person-years. Incident HIV infection was associated with younger age (AHR = 0.94; p = 0.003), being Latino (AHR = 2.44; p = 0.044), and/or being African American (AHR = 3.43; p = 0.046). Repeated NPEP use was not associated with incident HIV infection (AHR = 0.67; p = 0.26). Younger MSM of color who access NPEP, in particular, may benefit from early HIV risk-reduction and pre-exposure prophylaxis counseling.