Shoulder-related dysfunction affects individuals' ability to function independently and thus decreases quality of life. Functional task assessment is a key concern for a clinician in diagnostic assessment, outcome measurement, and planning of treatment programs. The purpose of this study was to test the reliability of the FASTRAK 3-dimensional (3-D) motion analysis and surface electromyography (sEMG) systems to analyze 3-D shoulder complex movements during functional tasks and compare motion patterns between subjects with and without shoulder dysfunctions (SDs).For the test, sEMG and 3-D motion analysis systems were used to characterize the functional tasks. Twenty-five asymptomatic male subjects and 21 male subjects with right shoulder disorders performed four functional tasks which involved arm reaching and raising activities with their dominant arms. Reliability was estimated by the intraclass correlation coefficient (ICC). Motion pattern was compared between two groups using mixed analysis of variances (ANOVAs). Shoulder complex kinematics and associated muscular activities during functional tasks were reliably quantified (ICC=0.83-0.99) from the means of three trials. Relative to the group without SDs, the group with SDs showed significant alteration in shoulder complex kinematics (3 degrees -40 degrees ) and associated muscular activities (3-10% maximum). Scapular tipping, scapular elevation, upper trapezius muscle function, and serratus anterior muscle function may have implications in the rehabilitation of patients with SDs.