Structural evidence of exercise-induced muscle disruption has traditionally involved histological analysis of muscle tissue obtained by needle biopsy, however, there are multiple limitations with this technique. Recently, diffusion tensor magnetic resonance imaging (DT-MRI) has been successfully demonstrated to noninvasively assess skeletal muscle abnormalities induced by traumatic injury. To determine the potential for DT-MRI to detect musculoskeletal changes after a bout of eccentric exercise, 10 healthy men performed 300 eccentric actions on an isokinetic dynamometer. DT-MRI measurements and muscle biopsies from the vastus lateralis were obtained before and 24 h post-exercise. Z-band streaming was higher 24 h post-exercise compared with baseline (P < 0.05). The histological indices of damage coincided with changes in DT-MRI parameters of fractional anisotropy (FA) and apparent diffusion coefficient; reflecting altered skeletal muscle geometry (P < 0.05). Z-band streaming quantified per fiber correlated with FA (r = -0.512; P < 0.05). DT-MRI can detect changes in human skeletal muscle structure following eccentric exercise.