PURPOSE: To describe factors associated with racial disparities in HIV (human immunodeficiency virus) incidence among men who have sex with men (MSM) in the United States. METHODS: In a longitudinal cohort of black and white HIV-negative MSM in Atlanta, HIV incidence rates were compared by race. Incidence hazard ratios (HRs) between black and white MSM were estimated with an age-scaled Cox proportional hazards model. A change-in-estimate approach was used to understand mediating time-independent and -dependent factors that accounted for the elevated HR. RESULTS: Thirty-two incident HIV infections occurred among 260 black and 302 white MSM during 843 person-years (PY) of follow-up. HIV incidence was higher among black MSM (6.5/100 PY; 95% confidence interval [CI]: 4.2-9.7) than white MSM (1.7/100 PY; CI: 0.7-3.3) and highest among young (18-24 years) black MSM (10.9/100 PY; CI: 6.2-17.6). The unadjusted hazard of HIV infection for black MSM was 2.9 (CI: 1.3-6.4) times that of white MSM; adjustment for health insurance status and partner race explained effectively all of the racial disparity. CONCLUSIONS: Relative to white MSM in Atlanta, black MSM, particularly young black MSM, experienced higher HIV incidence that was not attributable to individual risk behaviors. In a setting where partner pool risk is a driver of disparities, it is also important to maximize care and treatment for HIV-positive MSM.