The 2008 Institute of Medicine review of interventions research for posttraumatic stress disorder (PTSD) concluded that new, well-designed studies are needed to evaluate the efficacy of treatments for PTSD. The Department of Veterans Affairs (VA), the Department of Defense, and the National Institute of Mental Health convened a meeting on research methodology and the VA issued recommendations for design and analysis of randomized controlled clinical trials (RCTs) for PTSD. The rationale that formed the basis for several of the components of the recommendations is discussed here. Fundamental goals of RCT design are described. Strategies in design and analysis that contribute to the goals of an RCT and thereby enhance the likelihood of signal detection are considered.