We report a 72-year-old man with nevoid basal cell carcinoma syndrome (NBCCS) who presented with 25 skin cysts on his trunk and extremities. Fourteen of 25 skin cysts (56%) were observed on his hands. Histological examination demonstrated that most of the excised cysts had an epithelial wall with typical epidermal keratinization. However, 4 skin cysts (4/16; 25%) showed a corrugated or festooned inner surface of wall without a granular cell layer, which resembled an odontogenic keratocyst, a characteristic feature of skin cysts in NBCCS. A review of the literature suggested that acral localization of skin cysts is a distinctive feature of NBCCS. In addition, the histological findings of skin cysts resembling an odontogenic keratocyst might be a hallmark of NBCCS.