Identification of the hip joint centre (HJC) is important in the biomechanical examination of human movement. However, there is yet to be any published information regarding the influence of different HJC locations on hip and knee joint kinetics during functional tasks. This study aimed to examine the influence of four different HJC techniques on 3- D hip and knee joint kinetics/kinematics during the squat. Hip and knee joint kinetics/kinematics of the squat were obtained from fifteen male participants using an eight camera motion capture system. The 3-D kinetics/kinematics of the squat were quantified using four hip joint centre estimation techniques. Repeated measures ANOVAs were used to compare the discrete parameters as a function of each HJC location. The results show that significant differences in joint angles and moment parameters were evident at both the hip and knee joint in the coronal and transverse planes. These observations indicate that when calculating non-sagittal joint kinetics/kinematics during the squat, researchers should carefully consider their HJC method as it may significantly affect the interpretation of their data.