In some muscle diseases, such as muscular dystrophy, exercise can increase muscle damage and alter myofiber adaptation. We determined whether this is also true for the congenital muscle disease nemaline myopathy using our mouse model of this disease. Nemaline mice expressing a mutant alpha-tropomyosinslow protein [alpha-Tmslow(Met9Arg)] in skeletal muscle underwent 4 weeks of treadmill exercise. Exercise increased slow/oxidative myofibers, but different fibers were involved in these transformations in nemaline mice. Despite similar expression of the mutant alpha-Tmslow protein in muscles of the nemaline mouse, muscles responded in a unique manner that did not reflect fiber-type composition. For example, the particular fibers involved in fast-to-slow transformation were specific for each muscle examined. In contrast to the muscular dystrophies, exercise did not result in muscle damage nor did it cause an increase in rod-containing fibers; however, the fiber-type distribution of rod-containing fibers was altered in a muscle-specific fashion. That exercise did not exacerbate the pathology (i.e., nemaline rod formation) supports its use in nemaline myopathy patients. This study shows that fibers of a similar type respond to increased activity differently in different muscles and suggests that fibers of similar type may be functionally distinct in different muscles.