The association between different knee exertion injuries and lower limb malalignments was studied in 121 male athletes with knee exertion injuries and in 20 male athletes without knee symptoms. The associations between different malalignments was also analyzed. Leg length inequality (LLI), knee valgus, and different indexes of patellofemoral joint congruence were measured using radiological methods. Male athletes with patellar apicitis (n = 59) had significantly more LLI (P less than 0.001) and patella alta (P less than 0.05) than athletes without knee symptoms. The knee valgus was of the same numerical value in the shorter and longer leg sides in subjects with LLI of at least 5 mm (n = 58). A positive correlation was found between lateral patellar displacement (LPD) and patella alta (LT/LP) (P less than 0.001). Negative correlations were found between the sulcus angle (SA) and the lateral patello-femoral angle (LPA) (P less than 0.001) as well as between the LPD and the LPA (P less than 0.001).