In the past 30 years, the incarcerated population in the United States has more than quadrupled to 2.3 million adults. With an alarmingly high prevalence of mental illness, substance use, and other serious health conditions compounding their curtailed autonomy, prisoners constitute perhaps the nation’s most disadvantaged group. Scientifically rigorous research involving prisoners holds the potential to inform and enlighten correctional policy and to improve their treatment. At the same time, prisoner research presents significant ethical challenges to investigators and institutional review boards (IRBs) alike, by subjecting participants to conditions that potentially undermine the validity of their informed consent. In 2006, the Institute of Medicine Committee on Ethical Considerations for Revisions to the Department of Health and Human Services (DHHS) Regulations for Protection of Prisoners Involved in Research recommended both further protections and a more permissive approach to research review that would allow inmates greater access to potentially beneficial research. These recommendations have sparked renewed debate about the ethical trade-offs inherent to prisoner research. In this article, the authors review the major justifications for research with prisoner subjects and the associated ethical concerns, and argue that the field of empirical ethics has much to offer to the debate. They then propose a framework for prioritizing future empirical ethics inquiry on this understudied topic.