Of many approaches to reduce motion analysis errors, the compensation method of anatomical landmarks estimates the position of anatomical landmarks during motion. The method models the position of anatomical landmarks with joint angle or skin marker displacement using the data of the so-called dynamic calibration in which anatomical landmark positions are calibrated in ad hoc motions. Then the anatomical landmark positions are calibrated in target motions using the model. This study applies the compensation methods with joint angle and skin marker displacement to three lower extremity motions (walking, sit-to-stand/stand-to-sit, and step up/down) in ten healthy males and compares their performance. To compare the performance of the methods, two sets of kinematic variables were calculated using different two marker clusters, and the difference was obtained. Results showed that the compensation method with skin marker displacement had less differences by 30~60% compared to without compensation. And, it had significantly less difference in some kinematic variables (7 of 18) by 25~40% compared to the compensation method with joint angle. This study supports that compensation with skin marker displacement reduced the motion analysis STA errors more reliably than with joint angle in lower extremity motion analysis.