We analyzed data from a cohort of Black and Latino men who have sex with men (MSM) in order to identify correlates of prevalent and incident incarceration, including potential predictors related to their status as sexual and gender minorities (SGMs). Baseline and follow-up self-administered survey data were examined from Los Angeles County participants’ ages 18–45 years at enrollment who were either HIV negative or living with HIV, but recruited to over represent men who used drugs and men with unsuppressed HIV infection. Multivariable logistic regression models were developed to identify predictors of baseline incarceration history and of incident incarceration over study follow-up among 440 and 338 participants, respectively. Older age, Black race, low socioeconomic status, homelessness, stimulant use, and depression symptoms were associated with baseline incarceration history. The only SGM-related factor associated with baseline incarceration history was having experienced violence based on sexual orientation identity. Just one statistically significant, independent positive predictor of incident incarceration was identified: prior incarceration, whereas having four or more friends that could lend money was a statistically significant protective factor against incident incarceration. Fundamental Cause Theory provides a useful framework to explain identified predictors of incarceration. Addressing poverty, housing instability, inadequate access to health care, and their root causes is critical to reducing incarceration rates in this population, as is expanded access to both diversion and anti-recidivism programs and to evidence-based treatment for stimulant use disorders.