Background: Medical conditions often develop during military training. The aim of this study was to compile medical conditions and injuries sustained during a 5-day military exercise, compare them with incidences at similar civilian events, and subsequently identify differences between those who finished the exercise (Finishers) and those who did not (Nonfinishers) to identify preventable causes for not finishing and to reduce unnecessary health risks. Methods: Fifty-one soldiers had their blood parameters (creatine kinase [CK], aspartate transaminase [AST], alanine transaminase [ALT], gamma-glutamyl transferase [GGT], C-reactive protein [CRP], leukocytes, sodium), weight loss, and body temperature determined after the exercise. Additionally, the injuries and conditions that led the Nonfinishers to drop out were recorded. Results: The main reasons why Nonfinishers did not complete the exercise were physical exhaustion and minor injuries. After exercise, the Finishers showed only slightly increased incidence of hyponatremia, higher levels of CK, and significantly higher levels of AST, ALT, and CRP, and body weight loss. The Nonfinishers' results were significant for an elevated leukocyte count and lower mean temperatures. Conclusion: The specifics of military training did not influence the kind or the number of exertion-related medical conditions compared to similar civilian events. Both Finishers and Nonfinishers are at risk of developing exertion-related medical conditions such as rhabdomyolysis and hyponatremia. However, plain water did not increase the risk of exertional hyponatremia. Leukocytosis found in the Nonfinisher group could have been due to acute excessive exertion and, therefore, may be an indicator of general systemic fatigue. This could be used to differ between physical and psychological reasons for not finishing.