Musculoskeletal injuries (MSIs) occur frequently in military personnel. U.S. Marine Corps (USMC) recruits participate in an intense 13-week training program designed to transform civilians into basically trained Marines, during which they are susceptible to MSIs. Previous injury epidemiology research with USMC recruits was conducted in a non-gender-integrated training. Data for the current study were derived from a larger study, the USMC Gender-Integrated Recruit Training study, that was initiated to provide data-driven recommendations for gender integration during USMC recruit training. The purpose of the current analysis was to describe the unique profile of MSIs during USMC recruit training and compare MSIs between female and male recruits in gender-integrated training. Medical record-reviewed MSI data were obtained for recruits in three models of USMC recruit training: two models of gender-integrated recruit training at Marine Corps Recruit Depot (MCRD) Parris Island-the older Series Track (ST) model and the newer Integrated Company (IC) model, and a Male-Only (MO) cohort at MCRD San Diego. Incidence, anatomic region and subregion, event at the time of MSI, MSI type and onset, and disposition following MSI were described for each model. Group comparisons were conducted using Fisher's exact tests or independent samples t tests, as appropriate. MSI data were available for 584 recruits (ST: 98 female recruits, 95 male recruits; IC: 85 female recruits, 106 male recruits; MO: 200 male recruits). The cumulative incidence of MSIs was significantly higher among female compared to male recruits in the ST (59.2% vs. 29.5%, P < .001) and in the IC (25.9% vs. 12.3%, P = .023) cohorts. The most frequent anatomic location for MSIs was the lower extremity (female recruits: ST: 76.5% of MSIs, IC: 88.6%; male recruits: ST: 81.1%, IC: 80.0%, MO: 83.8%). The most frequent body part affected was the hip among female recruits (ST: 26.5% of MSIs, IC: 37.1%). The most frequent body part affected by MSIs among the male recruits was the knee in the ST (32.4%) and IC (53.3%) cohorts and the lower leg (27.0%) in the MO cohort. A significantly greater percentage of female compared to male recruits sustained a hip MSI in the ST (23.5% vs. 2.1%, P < .001) and IC (12.9% vs. 0.0%, P < .001) cohorts. There was no significant difference in knee MSI incidence between sexes in the ST (P = .323) or IC (P = .757) cohorts. A large percentage of MSIs resulted in light duty (female recruits: ST: 69.4% of MSIs, IC: 74.3%; male recruits: ST: 64.9%, IC: 73.3%, MO: 94.6%). This was the first study to assess the burden of MSIs concurrently among female and male USMC recruits in gender-integrated training. MSIs, especially those affecting the lower extremity, continue to occur frequently in this population. Female recruits are more susceptible to MSIs during USMC recruit training compared to male recruits and are especially prone to hip MSIs. Future research should focus on identifying modifiable risk factors for MSIs in this population, with a focus on reducing lower-extremity MSIs in all recruits and hip MSIs in female recruits.