This study examined the predictors of new incarceration and their association with HIV infection among 1278 black men who have sex with men enrolled and followed up in the HIV Prevention Trials Network 061 study. HIV Prevention Trials Network 061 was conducted to determine the feasibility and acceptability of a multicomponent intervention to reduce HIV infection among BMSM in 6 US cities. In this study, multivariable logistic regression models were used to explore the association between incarceration during study follow-up and several demographic, behavioral, and psychosocial variables at baseline found to be significant in bivariate analyses. In addition, Cox proportional hazard regression was used to explore the association between incarceration during study follow-up and incident HIV infection. Among the 1278 BMSM with follow-up data, 305 (24%) reported a new incarceration within 1 year of entering the study with an estimated incarceration incidence of 35% (95% confidence interval: 31% to 38%). After adjusting for confounders, lower education, lower annual income, previous incarceration frequency, and higher levels of perceived racism were significantly associated with new incarcerations during study follow-up. There was no observed association between incarceration during study follow-up and incident HIV infection. The very high level of new incarcerations highlights the importance of structural-level interventions to prevent incarceration among economically disenfranchised black men who have sex with men in the United States.