Peripheral nerve injuries are rarely followed by complete return of function. Deficits are particularly important for motor function, resulting in paralysis and muscle atrophy. In different groups, the sciatic nerve was either crushed or transected and repaired by direct suture or by tube repair using silicone or collagen tubes. After 60 days, nerve regeneration was assessed by electrophysiological and functional tests, nerve morphology and immunohistochemistry against choline acetyltransferase (ChAT) for labeling motor axons. Suture and tube repair resulted in similar levels of muscle reinnervation, but significantly lower than after nerve crush. Recovery of walking track pattern was poor in all groups after nerve section. The numbers of regenerated myelinated fibers and of ChAT+ fibers were similar to control values after nerve crush, but increased after section and repair. The normal fascicular architecture and grouping of ChAT+ fibers were maintained after nerve crush, but lost after section and repair, where motor fibers were scattered within small regenerated fascicles throughout the nerve. The loss of fascicular organization was related to the deficient recovery of locomotor function. Thus, labeling of motor axons by ChAT immunohistochemistry provides useful information for the study of the degree and specificity of nerve regeneration.