The knee is the most common site of running injuries, particularly prevalent in females. The purpose of this study was to clarify gender differences in the lower extremity kinematics during running, with a specific emphasis on the relationships between the distal and proximal factors and the knee joint kinematics. Eleven female and 11 male runners participated in this study. Three-dimensional marker positions were recorded with a motion analysis system while the subjects ran along a 25 m runway at a speed of 3.5 m/s. Kinematic variables were analyzed for the stance phase of the right leg. Female runners demonstrated significantly greater peak knee abduction (P<0.05), hip adduction (P<0.01) and internal rotation (P<0.05), whereas male runners demonstrated significantly greater peak rearfoot eversion (P<0.01). The knee abduction angles were positively correlated with hip adduction angles (r=0.49, P<0.05) and negatively correlated with rearfoot eversion (r= -0.69, P<0.001). There was no significant difference in normalised step width between genders (P>0.05). Smaller rearfoot eversion and greater hip adduction related closely to the greater knee abduction as the distal and proximal factors, respectively. These relationships are thought to be the compensatory joint motions in the frontal plane, because there was no significant difference in the normalised step width between females and males. The current results suggest that if the step width is identical, the subjects with greater knee abduction had smaller rearfoot eversion to compensate for greater hip adduction, which were more apparent in females. This explains greater knee abduction found in female runners, which can be linked to a high risk of knee injury.