Mullerian-type ciliated cysts are uncommon lesions usually found in the lower extremities and perineal region of young females. They have however been reported in males and in other anatomic sites. The cyst lining is typically positive for estrogen receptor (ER), progesterone receptor (PR), PAX-8, and WT1 immunohistochemical stains. This staining pattern has led to the notion that these cysts are of Müllerian origin. The vast majority of cases are located in the dermis where the preferred nomenclature is cutaneous ciliated cyst (CCC). We report a case of Müllerian-type ciliated cyst in the thigh of a 16-year-old girl. Unlike most of the cases reported in the English literature, this cyst was not centered in the dermis. Only a few other cases of Müllerian-type ciliated cysts with no cutaneous connection have been reported. We propose the term ectopic Müllerian cyst for this rare subset of lesions that are not skin based as is the current case.