This uncontrolled observational study examined the injury and medical discharge outcomes in 318 female and 1,634 male recruits as a result of changes to the Australian Army recruit physical training program. Changes included cessation of road runs, introduction of 400- to 800-m interval training, reduction in test run distance from 5 to 2.4 km, standardization of route marches, and the introduction of deep-water running. There was a 46.6% reduction in the rate of total injury presentation (chi 2 = 14.31, p = 0.0002) after the change. The annual rate of male medical discharges decreased 40.8% from 81.1/1,000 recruits in 1994/1995 to 47.0/1,000 recruits in 1995/1996 (chi 2 = 26.33, p = 0.0001). Female rates increased 58.3% from 104/1,000 recruits to 164.2/1,000 recruits (chi 2 = 6.09, p = 0.014). The decrease in the male medical discharge rate resulted in an estimated saving of $1,267,805 Australian. Bone scans were reduced by 50%, resulting in an estimated annual saving of $61,539 Australian. The disparity between male and female injury rates is a concern. The merits of mixed-gender physical training should be reviewed in the light of these observations, and the establishment of initial entry fitness standards for recruit training may need to be considered.