Background Some questionnaire studies have shown increased mental health problems, including probable post-traumatic stress disorder (PTSD), in soldiers deployed to Iraq. Aims To test prospectively whether such problems change over time and whether questionnaires provide accurate estimates of deployment-related PTSD compared with a clinical interview. Methods Dutch infantry troops from three cohorts completed questionnaires before deployment to Iraq (n=479), and about 5 months (n=382, 80%) and 15 months (n=331, 69%) thereafter. Posttraumatic stress disorder was evaluated by questionnaire and clinical interview. Results There were no group changes for general distress symptoms. The rates of PTSD for each cohort were 21, 4 and 6% based on questionnaires at 5 months. The deployment-related rates of PTSD based on the clinical interview were 4,3 and 3%. Conclusions There was a specific effect of deployment on mental health for a small minority Questionnaires eliciting stress symptoms gave substantial overestimations of the rate of PTSD.