Pilonidal disease consists of a hair-containing sinus or abscess occurring most frequently in intergluteal cleft. This disease is generally benign. Although very uncommon entity, it seems reasonable to be aware of possible malignancy in longstanding cases. We report a case of squamous cell carcinoma in a 52- year-old man, with a prolonged history of pilonidal disease and ulceration since 3 months before referring to our clinic. We excised the cyst, and the pathologic evaluation reported moderate differentiated squamous cell carcinoma. So, re-operation on the lesion site to excise a 2-cm margin was performed and the defect was covered with Limberg cutaneus flap. We recommend early excision of pilonidal cysts to prevent possible malignant degeneration. Histological examination of the excised materials to prevent missing rare malignant cases is recommended.