Infants with higher anorectal anomalies often develop fecal incontinence after surgical reconstruction mainly due to the incomplete development of defecation muscles. We investigated the possibility of defecation muscle regeneration by myoblast transplantation to improve fecal continence. Myoblasts from F344 female rats at ages of 1 day, 1, 2, 3, 4, 8, and 12 weeks were prepared by a preplating method. In vivo muscle differentiation of myoblasts was evaluated using immunofluorescence after transplantation of GFP-positive myoblasts into nude mice, the damaged thigh muscles, and the levator ani muscle of GFP-negative rats. The ratios of myoblasts obtained from 1 day, 1, 2, 3, 4, 8, and 12-week-old rats were 35, 71, 65, 61, 52, 44, and 23%, respectively. Myotube formation by transplanted myoblasts was observed in the back of nude mice. Myoblasts transplanted into damaged thigh muscles were integrated into recipient muscles with myofiber formation. Transferred myoblasts formed myotubes surrounding the levator ani muscle, although myofiber formation was not observed. Myoblasts were most efficiently obtained from juvenile rats. Myoblast transplantation may provide a novel treatment strategy for improving fecal continence after repair of anorectal anomalies in infants.