Background: The frequency and duration of deployments associated with increased morbidity is a significant concern for force health protection within the military population. Understanding the association between deployment and disability may provide a clearer understanding of factors adversely affecting U.S. military force readiness. Methods: A case-control analysis was conducted using records on enlisted active duty personnel in the Army and Marine Corps who were evaluated for a musculoskeletal disability and received a final disability disposition between FY 2003 and 2012. The study compared deployment, deployment frequency, and total time deployed in personnel who received musculoskeletal disability retirement to those with a musculoskeletal disability discharge other than retirement. Results: For females and males in either service, any deployment was associated with an increased risk of disability retirement (adjusted odds ratios [aOR] [95% confidence intervals (CI)]: males 1.76 [1.65-1.87]; females 1.41 [1.21-1.64]). Furthermore, increasing number of deployments (3+ deployments males aOR [95% CI]: 2.21 [1.92- 2.53]) and time spent deployed (24+ months Army Males aOR [95% CI]: 2.07 [1.79-2.40]) significantly increased the odds for disability retirement. Conclusion: Increasing frequency and duration of military deployments has an increased risk of disability retirement in service members with a musculoskeletal disability. Further research on this relationship is needed in a more representative sample of the U.S. military population.