Background It has been demonstrated that different degrees of pelvic floor muscle (PFM) maldevelop in anorectal malformations (ARMs); yet the development of satellite cells, the myogenic stem cells responsible for muscle growth, repair, and maintenance remains elusive during the embryogenesis of PFM. Striated muscle complex (SMC) is one of the most important components of PFM. The objective of this study was to observe the development pattern of satellite cells and their niche of SMC and investigate its possible role in PFM dysplasia in ARMs.