Background Musculoskeletal injuries during initial military training are a significant medical problem facing military organisations globally. In order to develop an injury management programme, this study aims to quantify the incidence and rehabilitation times for injury specific diagnoses. Methods This was a prospective follow-up study of musculoskeletal injuries in 6608 British Army recruits during a 26-week initial military training programme over a 2-year period. Incidence and rehabilitation times for injury specific diagnoses were recorded and analysed. Results During the study period the overall incidence of musculoskeletal injuries was 48.6%, and the most common diagnosis was iliotibial band syndrome (6.2%). A significant proportion of the injuries occurred during the first 11 weeks of the programme. The longest rehabilitation times were for stress fractures of the femur, calcaneus and tibia (116 ± 17 days, 92 ± 12 days, and 85 ± 11 days, respectively). The combination of high incidence and lengthy rehabilitation indicates that medial tibial stress syndrome had the greatest impact on training, accounting for almost 20% of all days spent in rehabilitation. Conclusion When setting prevention priorities consideration should be given to both the incidence of specific injury diagnoses and their associated time to recovery.