Physical training-related injuries are common among army recruits and other vigorously active populations, but little is known about their causation. To identify intrinsic risk factors, we prospectively measured 391 army trainees. For 8 weeks of basic training, 124 men and 186 women (79.3%) were studied. They answered questionnaires on past activities and sports participation, and were measured for height, weight, and body fat percentage; 71% of the subjects took an initial army physical training test. Women had a significantly higher incidence of time-loss injuries than men, 44.6% compared with 29.0%. During training, more time-loss injuries occurred among the 50% of the men who were slower on the mile run, 29.0% versus 0.0%. Slower women were likewise at greater risk than faster ones, 38.2% versus 18.5%. Men with histories of inactivity and with higher body mass index were at greater injury risk than other men, as were the shortest women. We conclude that female gender and low aerobic fitness measured by run times are risk factors for training injuries in army trainees, and that other factors such as prior activity levels and stature may affect men and women differently.