Rhabdomyomatous mesenchymal hamartoma (RMH) is a rare tumour-like lesion, which occurs in the skin of newborns, principally of the face and neck. RMH has also been reported in unusual sites, including oral cavity, nasal vestibule and vagina. In this case report we describe a rare case of RMH arising as a nodular mass at the anal margin of a male newborn. This is an unusual site for such a rare lesion. The histological examination of the lesion showed the typical features of RMH. Desmin and S100 expression has been determined by immunohistochemical analyses to assess the distribution of the mature skeletal muscle cells and small-sized nerves, which represented the principal components of the nodular mass. Our case emphasizes the possibility that RMH may occur in the perianal region and awareness of this possibility is crucial for pathologists to avoid confusion with other skeletal muscle-containing lesions, especially rhabdomyosarcoma.