The purpose of this study was to investigate the influences of isometric training at different joint angles on the muscle size and function of the human muscle-tendon complex in vivo. Furthermore, we tried to gain a better understanding of the mechanisms involved in angle specificity after isometric training from the aspect of neuromuscular adaptation and the changes in the properties of the muscle-tendon complex. Nine males completed 12-week unilateral training program (70% of maximal voluntary contraction (MVC) x 15 s x six sets) on the knee extensors at 50 degrees (shorter muscle length: ST) and 100 degrees (longer muscle length: LT). The internal muscle force (mechanical stress) is higher at 100 degrees than at 50 degrees because of the difference in the moment arm length, although there were no difference in the relative torque level, contraction and relaxation times, and repetition between ST and LT. Before and after training, isometric strength at eight angles and muscle volume were determined. Tendon elongation of knee extensors was measured by ultrasonography. There was no significant difference in the rate of increment of muscle volume between the protocols. Tendon stiffness increased significantly for LT, but not for ST. Although significant gain was limited to angles at or near the training angle for ST, increases in MVC at all angles were found for LT. These results suggest that only mechanical stress (internal muscle force imposed on muscle and tendon) contributes to adaptation in the tendon stiffness, although metabolic (relative torque level, etc.) and mechanical stress relate to muscle hypertrophy. Furthermore, increment of tendon stiffness for LT might contribute to increase torque output at smaller angles other than the training angle.