This study examined the predictors of new incarceration and its association with HIV infection among 1,278 Black men who have sex with men (BMSM) enrolled and followed in the HIV Prevention Trials Network (HPTN) 061 study. HPTN 061 was conducted to determine the feasibility and acceptability of a multi-component intervention to reduce HIV infection among BMSM in six U.S. cities. In the current 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 1,278 BMSM with follow-up data, 305 (24%) reported a new incarceration within one year of entering the study with an estimated incarceration incidence of 35% (95% CI: 31% - 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 highlight the importance of structural-level interventions to prevent incarceration among economically disenfranchised Black MSM in the United States.