The incidence of foot blisters and other overuse injuries of the lower limb is very high during basic military training (BMT). One hundred and eighty-nine subjects were divided into two intervention groups wearing alternative sock systems and one control group. Overall, 57% of the 173 recruits who completed the training, developed foot blisters. Binary logistic regression revealed the type of sock, race, previous hiking or military experience, and known orthopedic foot conditions to be predictive variables for foot blisters. Fifty-three percent of the 173 recruits also developed another overuse injury of the lower limb (25.4% related to the knee joint). Previous military or hiking experience and the association of foot blisters revealed to be predictive for the overuse injuries of the knee joint. The results of the present study suggest associated foot blisters are also an important factor in the development of overuse injuries of the knee joint during BMT.