Minimizing artifacts from skin movement is vital for acquiring more accurate kinematic data in human movement analysis. There are several stages that cause skin movement artifacts and these stages depend on the selection of the reference system, the error reduction method and the coordinate system in clinical gait analysis. Due to residual errors, which are applied to the Euler and Bryant angle methods in each stage, significant cumulative errors are generated in the motion analysis procedure. Thus, there is currently a great deal of research focusing on reducing kinematic errors through error reduction methods and kinematic error estimations in relation to the reference system. However, there have been no studies that have systematically examined the effects of the selected coordinate system on the estimation of kinematic errors, because most of these previous studies have been mainly concerned with the analysis of human movement using only the human models that are provided in the commercial 3D motion capture systems. Therefore, we have estimated the differences between the results of human movement analyses using an absolute coordinate system and a relative coordinate system during a gait, in order to establish which system provides a more accurate kinematic analysis at the ankle joint. Six normal adult subjects with no neurological or orthopedic conditions, lower extremity injuries, or recent history of lower extremity surgery were used in this study. The analysis was conducted at a walking speed of 1.35m/s. For the clinical estimation, we used a cardinal plane based on the segmental reference system and the differences were plotted on the planes. From this analysis, when a relative coordinate system was in the gait analysis, the average kinematic error occurring during the gait was determined to be 13.58mm, which was significantly higher than the error generated with an absolute coordinate system. Therefore, although the relative coordinate system can also be used to calculate the ankle joint center during the clinical gait analysis, the absolute coordinate system should be employed in order to obtain more accurate joint kinematic data. In addition, the results from this study can be used as a basis to select an appropriate coordinate system with regards to the diagnostic accuracy level required for various kinds of gait disorders.