Military deployment may adversely affect not only returning veterans, but their families, as well. As a result, researchers have increasingly focused on identifying risk and protective factors for successful family adaptation to war-zone deployment, re-integration of the returning veteran, and the longer-term psychosocial consequences of deployment experienced by some veterans and families. Post-traumatic stress disorder (PTSD) among returning veterans may pose particular challenges to military and military veteran families; however, questions remain regarding the impact of the course of veteran PTSD and other potential moderating factors on family adaptation to military deployment. The Family Foundations Study builds upon an established longitudinal cohort of Army soldiers (i.e. the Neurocognition Deployment Health Study) to help address remaining knowledge gaps. This report describes the conceptual framework and key gaps in knowledge that guided the study design, methodological challenges and special considerations in conducting military family research, and how these gaps, challenges, and special considerations are addressed by the study.