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The conflict in Afghanistan has exposed more Canadian Forces personnel to a greater degree of adversity than at any time in recent memory. We determined the incidence of Afghanistan deployment–related mental disorders and associated risk factors among personnel previously deployed in support of this mission.The study population consisted of 30 513 Canadian Forces personnel who began a deployment in support of the mission in Afghanistan before Jan. 1, 2009. The primary outcome was a mental disorder perceived by a Canadian Forces clinician to be related to the Afghanistan deployment. Data on diagnoses and perceptions were abstracted from medical records of a stratified random sample of 2014 personnel. Sample design weights were used in all analyses to generate descriptive statistics for the entire study population.Over a median follow-up of 1364 days, 13.5% (95% confidence interval [CI] 12.1%–14.8%) of the study population had a mental disorder that was attributed to the Afghanistan deployment. Posttraumatic stress disorder was the most common diagnosis (in 8.0%, 95% CI 7.0%–9.0%, of personnel). Deployment to higher-threat locations, service in the Canadian Army and lower rank were independent risk factors associated with an Afghanistan-related diagnosis (e.g., hazard ratio for deployment to Kandahar Province 5.6, 95% CI 2.6–12.5, relative to deployment to the United Arab Emirates). In contrast, sex, Reserve Forces status, multiple deployments and deployment length were not independent risk factors.An important minority of Canadian Forces personnel deployed in support of the Afghanistan mission had a diagnosis of a mental disorder perceived to be related to the deployment. Determining long-term outcomes is an important next step.