Introduction Musculoskeletal injuries to the lower extremities are major factors contributing to drop out from military tasks. The aim of the present study was to determine the incidence of musculoskeletal injuries and the parameters that differentiate between the soldiers who incurred these injuries and those who did not along 14 weeks of an infantry commanders course. Methods One-hundred and sixty-eight participants were recruited from an infantry commanders course. The soldiers were tested before (pre), in the middle (middle) and at the end (last) of the course for anthropometric measurements, proprioceptive ability and dynamic postural balance (DPB), and filled out an ankle stability questionnaire (Cumberland Ankle Instability Tool (CAIT). A physiotherapist followed and recorded all musculoskeletal injuries incurred by the participants during the course. Results Fifty-eight participants out of the 168 (34.5%) reported some pain/injury. Time effects were found for body mass index, DPB asymmetry, DPB in posterior-medial (P-M) direction and proprioception ability. Injury effects were found for DPB asymmetry, DPB in P-M direction, CAIT and proprioception ability. An interaction was found for proprioception ability. The Cox regression showed that the variables that are mostly effecting injuries were pretesting proprioception ability, DPB asymmetry and CAIT. Conclusions More than one out of three participants incurred musculoskeletal injuries, with deficits in proprioception ability, DPB and ankle stability in pretesting as major factors contributing to injuries. Further studies should look at the effect of specific exercises such as proprioception, DPB and ankle stability exercises for prevention and treatment of musculoskeletal injuries among combat soldiers.