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Soft tissue artifact is known to be one of the main sources of errors in motion analysis by means of stereophotogrammetry. Among many approaches to reduce such errors, one is to estimate the position of anatomical landmarks during a motion with joint angle or displacement of skin markers, which is the so-called compensation method of anatomical landmarks. The position of anatomical landmarks was modeled from the data of the so-called dynamic calibration, in which anatomical landmark positions are calibrated in an ad hoc motion. This study aimed to apply 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 compare their reliability. To compare the methods, two sets of kinematic variables were calculated using two different 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. In addition, it had significantly less difference in some kinematic variables (7 of 18) by 25–40% compared to the compensation method with joint angle.