The clinical features of merosin-positive congenital muscular dystrophy (CMD) and merosin-deficient CMD are well known, with those of merosin-deficient CMD being more severe. Whether the severity of histopathological findings correlates with these clinical features remains unanswered. In this study, the clinical and histopathological findings of 39 merosin-deficient and 37 merosin-positive CMD patients were compared. Merosin-deficient CMD patients were found to be younger, with earlier onset of symptoms, age of diagnosis, and a more severe clinical state (reflecting maximum motor capacity and contractures). On histopathological evaluation, endomysial fibrosis, perimysial fibrosis, and histopathological state (reflecting fibrosis, adiposis, necrosis, and variation in fiber size) were more severe in merosin-deficient CMD. There was a correlation between clinical and histopathological states only in merosin-deficient CMD.