Background
Malignant transformation arising from pilonidal cyst is a rarely reported condition associated with chronic inflammation. Treatment of pilonidal cyst with deep sinus tracts involves extensive ablation of adjacent structures to achieve tumor-free margins.

Case presentation
A 72-year-old woman came to our center for assessment of a cystic fluctuant mass over sacrococcygeal area. She also noted purulent discharge and erythematous swelling. The findings supported the diagnosis of pilonidal cyst with abscess; thus incision and drainage were performed. However, the lesion showed poor regression with persisted discharge, complicated with deep sinus tract and cutaneous horn formations. After en-bloc excision, histopathology findings confirmed the diagnosis of squamous cell carcinoma. Based on multidisciplinary team approach, she received tumor wide excision with concurrent laparoscopic abdominoperineal resection of the rectosigmoid colon, and permanent end colostomy. The defect was reconstructed with a superior gluteal artery perforator flap. No evidence of tumor recurrence or metastasis were found at follow up.

Conclusion
This is a rare case of malignant transformation arising from chronic pilonidal cyst. A diagnosis of malignancy should be considered for patients with long standing lesions and abnormal clinical patterns. Standard treatment is surgical wide excision. The superior gluteal artery perforator flap can be implemented for such sacrococcygeal defects with good results.