The main aim of this study was to assess the mental health status of the Navy Special Forces and regular forces three and a half years after the end of combat operations in mid 2009, and compare it with the findings in 2009. This cross sectional study was carried out in the Sri Lanka Navy (SLN), three and a half years after the end of combat operations. Representative samples of SLN Special Forces and regular forces deployed in combat areas were selected using simple random sampling. Only personnel who had served continuously in combat areas during the one year period prior to the end of combat operations were included in the study. The sample consisted of 220 Special Forces and 275 regular forces personnel. Compared to regular forces a significantly higher number of Special Forces personnel had experienced potentially traumatic events. Compared to the period immediately after end of combat operations, in the Special Forces, prevalence of psychological distress and fatigue showed a marginal increase while hazardous drinking and multiple physical symptoms showed a marginal decrease. In the regular forces, the prevalence of psychological distress, fatigue and multiple somatic symptoms declined and prevalence of hazardous drinking increased from 16.5% to 25.7%. During the same period prevalence of smoking doubled in both Special Forces and regular forces. Prevalence of PTSD reduced from 1.9% in Special Forces to 0.9% and in the regular forces from 2.07% to 1.1%. Three and a half years after the end of combat operations mental health problems have declined among SLN regular forces while there was no significant change among Special Forces. Hazardous drinking among regular forces and smoking among both Special Forces and regular forces have increased.