The purpose of this study was to determine the effects of shoulder muscle fatigue on three dimensional scapulothoracic and glenohumeral kinematics. Twenty healthy subjects participated in this study. Three-dimensional scapulothoracic and glenohumeral kinematics were determined from electromagnetic sensors attached to the scapula, humerus, and thorax. Surface electromyographic (EMG) data were collected from the upper and lower trapezius, serratus anterior, anterior and posterior deltoid, and infraspinatus muscles. Median power frequency (MPF) values were derived from the raw EMG data and were used to indicate the degree of local muscle fatigue. Kinematic and EMG measures were collected prior to and immediately following the performance of a shoulder elevation fatigue protocol. Following the performance of the fatigue protocol subjects demonstrated more upward and external rotation of the scapula, more clavicular retraction, and less humeral external rotation during arm elevation. All muscles with the exception of the lower trapezius showed EMG signs of fatigue, the most notable being the infraspinatus and deltoid muscles. In general, greater scapulothoracic motion and less glenohumeral motion was observed following muscle fatigue. Further studies are needed to determine what effects these changes have on the soft tissues and mechanics of the shoulder complex.