Branchial cleft cysts typically are characterized as lateral swellings anterior to sternocleidomastoid muscle in upper third of the neck. However, cysts have been reported in unusual location such as the thymus, oral cavity, parotid gland, pancreas, and thyroid. Perithyroidal branchial cleft cysts are also rare and preoperative diagnosis is very difficult. Recently we have experienced a case of intrathyroidal branchial cleft cys and a case of perithyroidal branchial cleft cyst, which were diagnosed preoperatively as the parathyroid cyst. So, we report these two cases with review of the literatures.