Occupational risks in everyday military service are often underestimated as compared to the risks faced during military missions. However, long-term exposure to “common” hazards can lead to chronic illness or, more importantly, affect person’s fitness for military service. A survey of work environment and health risks of Estonian Defence Forces (EDF) was initiated to assess health status and occupational exposures among military personnel in Estonia. A questionnaire was developed to assess self-perceived health and work environment in active service. A web-based questionnaire was sent to all servants of EDF in March 2015. Altogether 788 persons completed the questionnaire. The majority of respondents were male (87.0%) and had a service time over 9 years (67.8%). Self-rated health was assessed as good or very good by 63.8%. The most frequent exposures reported were electromagnetic fields, camouflage pastes, smokes and static work in forced positions. Although the majority (79.8%) was satisfied with their work environment in general, there were higher-risk structural units reporting dissatisfaction or health-related problems (Scouts Battalion, Artillery Battalion, Navy). Health problem during last 12 months limiting their usual activities was reported by 40% of respondents. Injuries causing temporary sick-leaves occurred in 10% of subjects, and they were mainly associated with shooting- or vehicle-related occupations. The most frequent health complaints, associated with work environment, were eye irritation, joint, low-back and neck-shoulder pain and unexplained fatigue. Hearing loss in the last 3 years was reported by 37.7%. Stress and anxiety symptoms occurred in 14.8% and it was associated with service in Special Operations Unit, Intelligence Centre and Artillery Battalion. Overall, the self-reported health status, satisfaction with service and work environment was rated highly among military personnel. In spite of positive results, there are units inside EDF with considerably higher occupational exposures, dissatisfaction of work conditions and consequent health problems.