Background: In military basic training, stress fractures are a common orthopedic problem. Female recruits have a significantly higher incidence of stress fractures than do male recruits. Because the Israeli Defense Forces opened traditionally male roles in combat units to female recruits, their high risk for stress fractures is of concern. Objective: To compare the prevalence of stress fractures during Israeli Defense Forces anti-aircraft basic training among otherwise healthy young male and female recruits, in terms of anatomic distribution and severity. Design: Ten mixed gender batteries, including 375 male recruits and 138 female recruits, carried out basic training in the Israeli anti-aircraft corps between November 1999 and January 2003. Each battery was monitored prospectively for 10 weeks of a basic training course. During that time, recruits who were suspected of having an overuse injury went through a protocol that included an orthopedic specialist physical examination followed by a radionuclide technetium bone scan, which was assessed by consultant nuclear medicine experts. The assessment included the anatomic site and the severity of the fractures, labeled as either high severity or low severity. Results: Stress fractures were significantly more common among female recruits than among male recruits. A total of 42 male (11.2%) and 33 female (23.91%) recruits had positive bone scans for stress fractures (female:male relative ratio, 2.13; p < 0.001). Pelvic, femur, and tibia fractures were significantly more common among female recruits than among male recruits (p < 0.005). Female recruits had significantly more severe fractures in the tibia (p < 0.05). However, there was no significant difference in the severity of stress fractures in the femur or metatarsals between male and female recruits, as assessed by radionuclide uptake. Conclusions: We recommend that different training programs be assigned according to gender, in which female recruits would have a lower level of target strain or a more moderate incline of strain in the training program throughout basic training.