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Young men who have sex with men (MSM) and MSM of color have the highest HIV incidence in the United States. To explore possible explanations for these disparities and known individual risk factors, we analyzed the per contact risk (PCR) of HIV seroconversion in the early highly active antiretroviral therapy era.Data from 3 longitudinal studies of MSM (HIV Network for Prevention Trials Vaccine Preparedness Study, EXPLORE behavioral efficacy trial, and VAX004 vaccine efficacy trial) were pooled. The analysis included visits where participants reported unprotected receptive anal intercourse (URA), protected receptive anal intercourse, or unprotected insertive anal intercourse (UIA) with an HIV seropositive, unknown HIV serostatus, or an HIV seronegative partner. We used regression standardization to estimate average PCRs for each type of contact, with bootstrap confidence intervals.The estimated PCR was highest for URA with an HIV seropositive partner (0.73%; 95% bootstrap confidence interval [BCI]: 0.45% to 0.98%) followed by URA with a partner of unknown HIV serostatus (0.49%; 95% BCI: 0.32% to 0.62%). The estimated PCR for protected receptive anal intercourse and UIA with an HIV seropositive partner was 0.08% (95% BCI: 0.0% to 0.19%) and 0.22% (95% BCI: 0.05% to 0.39%), respectively. Average PCRs for URA and UIA with HIV seropositive partners were higher by 0.14%–0.34% among younger participants and higher by 0.08% for UIA among Latino participants compared with white participants. Estimated PCRs increased with the increasing number of sexual partners, use of methamphetamines or poppers, and history of sexually transmitted infection.Susceptibility or partner factors may explain the higher HIV conversion risk for younger MSM, some MSM of color, and those reporting individual risk factors.