Abstract War experiences are associated with the risk of long-term mental health problems. The War-affected Youths (WAYS) Study comprises a cohort of 539 youths (61% female) aged between 18 to 25 (at baseline) randomly sampled from the population of war-affected youths in northern Uganda. The study aims to chart the trajectory of long-term mental health consequences of war and the roles of individual, family, and community contextual risk and protective factors in influencing the course of mental health using Social Ecology Model, thus, addressing both the individual and its social ecology. Knowledge of postwar contexts may inform policy and guide interventions on postwar psychosocial adjustment and reintegration in conflict-prone Great Lakes region of Africa (Rwanda, Burundi, DR Congo, Uganda, Central African Republic, and South Sudan). Two waves of data collection have been conducted and more data collection is planned. At baseline, information on demographic characteristics, pre-war experiences, psychosocial outcomes, coping, stigma/discrimination, family and community acceptance and relationship, family functioning, and post-war experiences were obtained. At follow-up, information on general health, gender-based violence, PTSD, social skills, trauma memory quality, rumination, self-esteem, and psychosocial outcomes were collected. Approval to access the data can be obtained on application to the Principal Investigator upon submission of a research proposal with ethical approval from the applicant's institution. This research is funded by Wellcome Trust and Gulu University.