Research on military populations indicates that failure to complete training is a significant problem for armed forces around the world. The present study estimated the prevalence of musculoskeletal complaints or injuries and potential individual risk factors leading to premature discharge from Swedish military service. Male conscripts, n=469 answered a questionnaire and performed physical tests at the start of their military service. A high prevalence of complaints or injuries in lower back and knee was shown. Logistic regression analyses showed an increased risk of discharge (odds ratio, OR) when reporting current complaints or injuries in any part of the body (OR 4.6), being physically inactive (OR 2.0), cigarette smoking (OR 2.7), or poor mental health (OR 3.6). The findings highlight the need for improved preenlistment examination and/or early preventive strategies addressing both physical and psychological interventions.