Objective: Strenuous physical activity, such as military training, is known to demand a high degree of physical performance and to cause overuse injuries. However, the exact relation between injury incidence and physical fitness level and the influence of military training on measures of functional performance, such as intermittent endurance capacity and maximal jump performance, are not fully described.Methods: A total of 330 military conscripts were prospectively followed during military basic training. They were divided into 4 self-assessed physical fitness level groups (well trained, trained, less trained, and untrained) and underwent physical performance tests together with registration of injury incidence.Results: Twelve weeks of military basic training was found to result in an overall injury rate of 28%, with an inverse relation between physical fitness level and incidence of overuse injury (P < 0.0001). Furthermore a fourfold higher injury rate was observed in the previously untrained soldiers compared with the well-trained soldiers. An increase in intermittent endurance capacity (20-m intermittent shuttle run test) was seen in all groups, (13 to 62%, P < 0.05), whereas only the previously untrained group of soldiers improved in aerobic capacity (8 and 16%, P < 0.05; maximal oxygen uptake and Coopers 12-minute running test). Maximal jump performance, both with and without backpack loading (15 kg), decreased (5 to 13%, P < 0.05) in 93% of the soldiers despite weight loss.Conclusions: Military basic training has a positive effect on intermittent endurance capacity but a detrimental effect on jump performance. Furthermore, low levels of physical fitness are strongly associated with proneness toward overuse injury development in soldiers going through intense training.