Incarceration is a crisis among African Americans, and the prevalence of HIV/AIDS in incarcerated men and women is 3-5 times that of the general population. We explore the potential implications of the widespread incarceration of African Americans on HIV risk and HIV outcomes in: 1) the current and formerly incarcerated, 2) their sexual partners, and 3) the communities impacted by incarceration. We set forth a research agenda for understanding and ameliorating the negative impacts incarceration and conclude that the African-American population's ability to successfully address the HIV/AIDS epidemic requires a coordinated and evidence-based response to the challenge of effectively preventing, managing and treating HIV in populations affected by incarceration.