Primary branchial cleft cyst carcinoma is very rare and it arises in preexisting branchial cleft cyst. It is very important to rule out metastatic squamous cell carcinoma in cervical lymph node and there are strict criteria to diagnose this unique disease entity. Presence of benign ciliated epithelial cells in cystic surface is very important clue to confim the diagnosis. The causal relationshiop of human papilloma virus is not proven yet but HPV16 was detected in this case.