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BACKGROUND: Although it has been posited that exposure to adverse childhood experiences (ACEs) increases vulnerability to deployment stress, previous literature in this area has demonstrated conflicting results. Using a cross-sectional population-based sample of active military personnel, the present study examined the relationship between ACEs, deployment related stressors and mood and anxiety disorders. METHOD: Data were analyzed from the 2002 Canadian Community Health Survey-Canadian Forces Supplement (CCHS-CFS; n = 8340, age 18-54 years, response rate 81%). The following ACEs were self-reported retrospectively: childhood physical abuse, childhood sexual abuse, economic deprivation, exposure to domestic violence, parental divorce/separation, parental substance abuse problems, hospitalization as a child, and apprehension by a child protection service. DSM-IV mood and anxiety disorders [major depressive disorder, post-traumatic stress disorder (PTSD), generalized anxiety disorder (GAD), panic attacks/disorder and social phobia] were assessed using the composite international diagnostic interview (CIDI). RESULTS: Even after adjusting for the effects of deployment-related traumatic exposures (DRTEs), exposure to ACEs was significantly associated with past-year mood or anxiety disorder among men [adjusted odds ratio (aOR) 1.34, 99% confidence interval (CI) 1.03-1.73, p < 0.01] and women [aOR 1.37, 99% CI 1.00-1.89, p = 0.01]. Participants exposed to both ACEs and DRTEs had the highest prevalence of past-year mood or anxiety disorder in comparison to those who were exposed to either ACEs alone, DRTEs alone, or no exposure. CONCLUSIONS: ACEs are associated with several mood and anxiety disorders among active military personnel. Intervention strategies to prevent mental health problems should consider the utility of targeting soldiers with exposure to ACEs.