1020 soldiers undergoing 3 months of basic military training were randomized to undergo the prevention program consisting of exercises for strength, flexibility, and coordination, or the placebo program. A physical training program focused on muscular strengthening, coordination and flexibility, based on the intrinsic risk factors was identified by literature review. The purpose of this study was to determine whether the aforementioned program, when combined with an increase in physical activity, can reduce the incidence of overuse knee injuries and medial tibial stress syndrome. Results indicated that it did not impact the risk of developing overuse knee injuries or medial tibial stress syndrome in soldiers undergoing an increase in physical activity. The training program, however, increased maximal running distance in a 12-minute run test.