The relationship between trunk and lower limb kinematics in healthy females versus males is unclear since trunk kinematics in the frontal and transverse planes have not been systematically examined with lower limb kinematics. The aim of this study was to investigate the existence of different multi-joints movement strategies between genders during a single leg squat. We expected that compared to males, females would have greater trunk and pelvis displacement due to less trunk control and display hip and knee movement consistent with medial-collapse (i.e. greater hip adduction, hip medial rotation, knee abduction, and knee lateral rotation) on the weight-bearing limb. Nine females and 10 males participated in the study. Kinematic data were collected using an 8-camera, 3D-motion-capture-system. Trunk relative to pelvis, pelvis relative to the laboratory, hip and knee angles in three planes (sagittal, frontal and transverse) were examined at two time events relevant to knee joint mechanics: 45° of knee flexion and peak knee flexion. Females flexed their trunk less than males and rotated their trunk and pelvis toward the weight-bearing limb more than males. Females also displayed greater hip adduction and knee abduction than males. Taken together these results suggest that females and males used different movement strategies during a single leg squat. Females displayed a trunk and pelvic movement pattern that may put them at risk of knee injury and pain.