BackgroundTeam handball involves a tremendous amount of shoulder motion with high forces during repeated extended external range of motion. Shoulder complaints are a common problem in youth handball players. While eccentric training for the lower extremity shows preventive effects by improving strength, range of motion and fascicle length, there is a research gap for the shoulder joint and for advanced tissue characterization using diffusion tensor imaging.ObjectivesTo investigate the effects of six-week eccentric isokinetic resistance training on the strength, flexibility, and fiber architecture characteristics of the external rotators compared to an active control group in junior handball players.Methods15 subjects were randomly assigned to the eccentric training group and 14 subjects to the active control group (conventional training). Primary outcome measures were eccentric and concentric isokinetic strength of the external rotators, range of motion, and muscle fascicle length and fascicle volume.ResultsThe intervention group, showed significant changes in eccentric strength (+15 %). The supraspinatus and infraspinatus muscles showed significant increases in fascicle length (+13 % and +8 %), and in fractional anisotropy (+9 % and 6 %), which were significantly different from the control group.ConclusionsEccentric isokinetic training has a significant effect on the function and macroscopic structure of the shoulder external rotators in male junior handball players. While strength parameters and muscle structure improved, range of motion did not change. Future research is needed for more convenient field exercises in this context.