Measurement of 3D scapular kinematics is meaningful in patients with shoulder pathologies showing scapular dyskinesis. This study evaluates the effect of single and double anatomical calibration (0° and 120°) with a scapula locator compared to standard calibration (using sensor alignment with the spina scapulae and static upright posture, ISEO-protocol) on 3D scapular kinematics measured with an inertial and magnetic measurement system (IMMS).Ten patients with scapular dyskinesis performed humeral anteflexion and abduction movements while 3D scapular kinematics were measured using IMMS sensors. The sensor on the scapula was anatomically calibrated (i) according to the ISEO-protocol, (ii) using single scapula locator calibration (0°) and (iii) double scapula locator calibration (0° and 120°). For calibration, the scapula locator (with IMMS) was positioned on the scapula, while holding the humerus at several anteflexion and abduction postures. Single and double calibration resulted in a significant increase of scapular anterior tilt (14-30°) with respect to the skin-fixed sensor (ISEO). Protraction angles were not significantly different. During anteflexion, double calibration did not show a significant increase in lateral rotation compared to single calibration. During abduction of > 90°, double calibration showed 10-14° increased lateral rotation with respect to single calibration, although this was not significant (P > 0.06).Calibration with a scapula locator when applying IMMS is necessary, because measures of scapular anterior tilt are grossly underestimated with the ISEO-protocol. For shoulder movements that exceed 90° elevation, a double calibration prevents small but relevant underestimation of lateral rotation angles of the scapula.