Objectives: To evaluate whether tobacco use, alcohol consumption, and weight gain are associated with the diagnosis of overuse musculoskeletal injuries within the first 12 months after lower limb amputation. Design: Retrospective cohort study. Setting: Military treatment facilities. Participants: Service members (N=681) with a deployment-related lower limb amputation. Interventions: Not applicable. Main Outcome Measures: Clinical diagnosis codes associated with musculoskeletal overuse injuries of the lower limb, upper limb, and low back regions. Results: In the first three months after amputation, tobacco use and alcohol consumption were reported in 55.7% and 72.0%, respectively, of the retrospective sample. The overall mean weight change was 22.9±23.6 pounds. The prevalence of reporting at least 1 overuse injury within 4 to 12 months after amputation was 57.0% in the sample, with prevalence rates of lower limb, upper limb and low back pain diagnoses at 28.3%, 21.7%, and 21.1%, respectively. Service members reporting tobacco use in the first 3 months after amputation were nearly twice as likely to be diagnosed with a lower limb musculoskeletal injury 4 to 12 months after amputation. Similarly, service members reporting alcohol consumption within the first 3 months after amputation were more than twice as likely to be diagnosed with at least 1 overuse musculoskeletal injury 4 to 12 months after amputation. However, weight change or maximum weight after amputation were not associated with the diagnosis of an overuse musculoskeletal injury. Conclusions: Development of secondary overuse musculoskeletal injury appears to be related to tobacco use and alcohol consumption, but not to weight gain. These findings warrant focused research efforts toward developing preventive interventions.