Skeletal muscle biopsies damage the muscle by completely removing a section of muscle fibers and their associated basal laminae. The purpose of this study was to observe the time course and extent of skeletal muscle regeneration in response to damage caused by a muscle biopsy and to determine whether these biopsied fibers re-establish continuity. Biopsies were taken bilaterally from the gastrocnemius muscles of 20 male Sprague-Dawley rats. The gastrocnemius muscles were then studied 0 (control), 3, 10, 20, 30, and 35 days after the biopsy (four rats at each time point). Each muscle was either cross- or longitudinally sectioned for immunohistochemical analysis of the damaged area. Sections were stained for either myosin heavy chain developmental isoform (MHCd) and type I collagen or muscle cadherin (Mcad). The pattern of muscle regeneration was similar to that reported in the literature describing “discontinuous” regeneration. The time course of regeneration was notably slower and significant connective tissue scarring was observed. Analysis of MHCd expression revealed extensive myotube formation by 10 days post-biopsy. By 35 days post-biopsy, most fibers had re-established continuity across the damaged area; however, cross sectional areas of these fibers were still significantly less than those of undamaged fibers (p<0.01). The deposition of collagen resulted in incomplete regeneration of fibers in the most superficial portion of the muscle. Both central myonuclei and satellite cell counts were significantly higher than controls over the length of the study (p<0.01). The number of myonuclei per fiber and myonuclei per mm fiber were significantly lower than controls at all time points (p<0.01). Cross sectional area per myonucleus was the only measure to return to control values by the end of the study. The lack of structural support and myogenic signals from the basal lamina and the dense collagen build-up most likely delayed the development of regenerating fibers. These results suggest that the size of the damaged area created by a muscle biopsy and the loss of the basal lamina significantly impair the regeneration process; however the biopsies do not cause permanent damage to most fibers.