The effect of anatomic variation on the risk of overuse injuries has not been adequately evaluated. To determine the association of several common anatomic characteristics (genu varum, genu valgum, genu recurvatum, and lower limb length differences) with risk of overuse injury, we made prospective morphologic measurements of young men prior to beginning 12 week of Army infantry training. The training included frequent running, marching, calisthenics, and other vigorous activities. Lower extremity anatomic landmarks were high-lighted, and front- and side-view photographic slides were taken of the 294 study volunteers. The slides were compute digitized, and the following measures calculated: pelvic width to knee width ratio (to assess genu valgum/varum), quadriceps angle (Q-angle), knee angle at full extension, and lower limb length differences. The cumulative incidence of lower limb overuse injury was 30%. Relative risk of (RR) of overuse injury was significantly higher among participants with the most valgus knees (RR = 1.9). Those with Q-angle of more than 15 degrees had significantly increased risk specifically for stress fractures (RR = 5.4). Anatomic characteristics were associated with several other types of injuries, including pain and nonacute muscle strain due to overuse. This pilot study provides evidence that some lower limb morphologic characteristics may place individuals at increased risk of overuse injuries.