Choledochal cysts (CC) are rare cystic dilatation of the biliary trees. Malignancy is one of the important significant findings in CC and its incidence increases with age. Associated squamous cell carcinoma of the choledochal cyst is an uncommon pathological finding.
We present a 21-year-old male diagnosed with type 1 CC and planned for excision of the cystic dilated extrahepatic biliary tract with hepaticojejunal anastomosis in Roux-en-Y but underwent pancreaticoduodenectomy due to intraoperative palpable mass of CC which was adhered to the duodenum and pancreatic head. Histopathology of the excised specimen revealed squamous cell carcinoma (SCC) of the choledochal cyst.
CC represents a rare biliary cystic disease. Though infrequent, malignant transformation in CC includes cholangiocarcinoma, adenocarcinoma, and rarely SCC. The post-operative management for SCC in CC is ill-defined and carries a grave prognosis.
The choledochal cyst should be completely excised wherever possible to avoid the possible malignant transformation in CC including SCC.

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