Federal, state, and local initiatives to improve the treatment and outcomes for young people in the juvenile justice system prompt the need for additional research. Despite the call for empirical data, researchers encounter numerous obstacles when initiating and conducting studies in detention and post-adjudication facilities. These obstacles are often only briefly mentioned in publications, but they can interfere with researchers' desires and abilities to conduct studies in these settings. This paper reviews legal, ethical, and methodological challenges to successfully conducting research in detention and residential post-adjudication placements, including selecting and accessing appropriate facilities, obtaining institutional review board approval, seeking parental permission and youth assent, reporting child abuse and neglect, responding to participants' threats to harm self or others, working effectively with facilities, juvenile justice system-related attrition, and the dissemination of research findings. Recommendations are presented to help investigators anticipate obstacles when designing and executing research protocols to prevent interference and to encourage ethical responses and successful study completion. Copyright © 2012 John Wiley & Sons, Ltd.