Early trunk rotation (ETR), which is a unique kinematics of the trunk that occurs during baseball throwing, is thought to be related to shoulder injuries. Pelvic rotation is a confounder when studying the effects of trunk rotation on shoulder biomechanics. The purpose of this study was to understand the "pure" effects of trunk rotation on shoulder biomechanics, with pelvic rotation under control. Our hypotheses were as follows: (1) throwers with ETR have a different shoulder kinematics pattern compared with throwers without ETR; (2) throwers with ETR have a lower ball speed performance than do throwers without ETR; and (3) throwers with ETR have a greater value of shoulder forces and moments, which may increase risks of shoulder injury, than do throwers without ETR. Fifty-seven elite throwers were enrolled and divided into 2 groups (non-ETR and ETR) using an outdoor motion analysis. Several kinematics and kinetics parameters of the shoulder were analyzed and compared between the 2 groups. Ball velocity was faster in the non-ETR group (127 km/h) compared with the ETR group (120 km/h). The shoulders of throwers in the ETR group showed pathokinematics of "horizontal adduction lag" and "dropped elbow." The increases in maximal posterior force, inferior force, horizontal abduction moment, and vertical adduction moment were 9.2%, 13.6%, 21.3%, and 24.3%, respectively, in the shoulders of throwers in the ETR group. These results indicate that ETR may be hazardous for the throwing shoulder. With lower ball velocity and higher shoulder joint loading, ETR is not a proper pitching pattern for kinetic energy transfer. Improper pitching mechanics among baseball throwers, such as ETR, may result in higher shoulder joint loading and increased risk of shoulder injuries. When treating throwers with shoulder injuries, it is important not only to address shoulder anatomy and pathology but also to understand the possible pathomechanics and pathogenesis of the shoulder caused by ETR. Furthermore, special training programs focusing on trunk flexibility and core muscle strengthening should be implemented to prevent ETR and decrease the risk of shoulder injuries. Motion analysis is useful for the screening and early detection of improper pitching mechanics in throwers.