A variety of physical characteristics of athletes has been proposed to be related to the risk to sustain a sports injury. The aim of the present study was to determine the influence of flexibility, anthropometric characteristics and malalignment of the lower extremities on the risk to sustain a sports injury, using a prospective study design and subjects exposed to rather equal extrinsic risk factors. Physical education students (N = 136) were followed during their four-year education. Sixteen flexibility indices, four anthropometric characteristics and five malalignment indices of the lower extremities were assessed at the start of the study and all sports injuries sustained in that four-year period were recorded. No influence of flexibility or anthropometric variables on the total number of injuries or the number of several specific injuries (ankle sprain, muscle rupture, dislocation, shin splints, backache) could be established. Malalignments of the lower extremities (average prevalence 18% and only minor deviations) did show some but inconsistent relations with the number of (specific) injuries. For pelvic obliquity it was positive as predicted, but for malalignment of the rearfoot and a deviant footprint it appeared to be negative. Leg length inequality and malalignment of the knees were not related to injuries. The most likely explanation for these (poor) findings is the relatively low number and great variety of sports injuries recorded. Further, the homogeneity in physical characteristics of the population under study makes it difficult to find significant relationships. A study design that meets both the criterium of similar extrinsic risk factors and that of a wide range of physical characteristics in a representative sporting population, however, is not practicable.