This study examined the effects of squatting with different foot positions on the muscle activation of the vastus medialis oblique (VMO) and vastus lateralis (VL) muscles in subjects with genu varum. Methods: Thirty four subjects participated in this study. Surface electromyography was used to measure the muscle activation of the VMO and VL muscles at the knee angles (15°, 60°) at three foot positions (internal rotation, neutral position, external rotation) during squatting. Results: Muscle activation differences at different knee angles and foot positions differed significantly between the VMO and VL muscles in both the varus and normal groups. In addition, there was a significant difference according to the knee angles with the foot in external rotation in the VMO and VL ratio. In the varus group, however, the VMO and VL ratio were significantly different only with the feet in internal rotation. In the muscle activation changes of the knee angle differences in the foot position, there was no significant difference in the varus group, but both the VMO and VL muscles were significant different in the normal group. Conclusion: In both groups, regardless of the foot position, muscle activation of the VMO and VL muscles increased with increasing knee flexion angle. In the normal group, when squatting with the feet in external rotation, the VMO and VL muscles activations increased with increasing knee angle. In the varus group, however, the foot position did not affect the VMO or VL muscle activation. This study shows that subjects with genu varum and normal subjects have different VMO and VL muscle activation patterns during squat exercises.