In morphological analysis of the femur, the hip joint centre (HJC) is generally determined using a 3D model of the femoral head based on medical images. However, the portion of the image selected to represent the femoral head may influence the HJC. We determined if this influence invalidates the results of three HJC calculation methods, one of which we introduce here. To isolate femoral heads in cadaver CT images, thresholds were applied to the distance between femur and acetabulum models. The sensitivity of the HJC to these thresholds and the differences between methods were quantified. For thresholds between 6 and 9 mm and healthy hips, differences between methods were below 1 mm and all methods were insensitive to threshold changes. For higher thresholds, the fovea capitis femoris disturbed the HJC. In two deformed hips, the new method performed superiorly. We conclude that for normal hips all methods produce valid results.