Military deployment to combat zones puts military personnel to a number of physical and mental challenges that may adversely affect mental health. Until now, few studies have been performed in Europe on mental health utilization after military deployment. We compared the incidence of mental health consultations with the Military Mental Health Service (MMHS) of military deployed to Afghanistan to that of non-deployed military personnel. We assessed utilization of the MMHS by the full cohort of the Netherlands Armed Forces enlisted between 2008 and 2010 through linkage of mental health and human resource information systems. The total population consisted of 50,508 military (18,233 deployed, 32,275 non-deployed), who accounted for 1,906 new consultations with the MMHS. The follow-up was limited to the first 2 years following deployment. We observed higher mental health care utilization in deployed vs. non-deployed military personnel; hazard ratio (HR), adjusted for sex, military branch and time in service, 1.84 [95% CI 1.61–2.11] in the first and 1.28 [1.09–1.49] in the second year after deployment. An increased risk of adjustment disorders (HR 2.59 [2.02–3.32] and 1.74 [1.30–2.32]) and of anxiety disorders (2.22 [1.52–3.25] and 2.28 [1.50–3.45]) including posttraumatic stress disorder (5.15 [2.55–10.40] and 5.28 [2.42–11.50]), but not of mood disorders (1.33 [0.90–1.97] and 1.11 [0.68–1.82]), was observed in deployed personnel in the first- and second-year post-deployment, respectively. Military personnel deployed in a unit with a higher risk of confrontation with potentially traumatic events had a higher HR (2.13 [1.84–2.47] and 1.40 [1.18–1.67]). Though absolute risk was low, in the first and second year following deployment to Afghanistan there was an 80 and 30% higher risk for mental health problems resulting in a consultation with the Dutch MMHS compared to military never deployed to Afghanistan. These observations underscore the need for an adequate mental health infrastructure for those returning from ...