African Americans face disproportionate sexually transmitted infection including HIV (STI/HIV), with those passing through a correctional facility at heightened risk. There is a need to identify modifiable STI/HIV risk factors among incarcerated African Americans. Project DISRUPT is a cohort study of incarcerated African American men recruited from September 2011 through January 2014 from prisons in North Carolina who were in committed partnerships with women at prison entry (N = 207). During the baseline (in-prison) study visit, participants responded to a risk behavior survey and provided a urine specimen, which was tested for STIs. Substantial proportions reported multiple partnerships (42 %), concurrent partnerships (33 %), and buying sex (11 %) in the 6 months before incarceration, and 9 % tested positive for an STI at baseline (chlamydia: 5.3 %, gonorrhea: 0.5 %, trichomoniasis: 4.9 %). Poverty and depression appeared to be strongly associated with sexual risk behaviors. Substance use was linked to prevalent STI, with binge drinking the strongest independent risk factor (adjusted odds ratio: 3.79, 95 % CI 1.19–12.04). There is a continued need for improved prison-based STI testing, treatment, and prevention education as well as mental health and substance use diagnosis.