A rare case of a clear cell adenocarcinoma and an adenosarcoma coexisting with a heterologous rhabdomyosarcoma in an endometriotic cyst of the ovary is reported. The tumor was composed of a cystic area and a solid area arising from the cyst wall. In the cystic lesion, a detached polypoid mass was also identified. The cyst wall was lined with a single layer of endometrial-type cells, whereas the solid area was composed of a clear cell adenocarcinoma. In the detached polypoid mass, an exophytic leaf-like pattern containing benign endometrial-type cells and squamous epithelial and rhabdomyosarcoma components, which were positive for desmin and myoglobin, was observed. Using X-chromosomal clonality assay, these clear cell adenocarcinoma and adenosarcoma components showed patterns of polyclonality. To the authors' knowledge, this is the first reported case of a clear cell adenocarcinoma and an adenosarcoma coexisting with heterologous rhabdomyosarcoma in an endometriotic cyst of the ovary.