A branchial cleft cyst or simply branchial cyst is a cyst as a swelling in the upper part of neck anterior to sternocleidomastoid. It can, but does not necessarily, have an opening to the skin surface, called a fistula. The cause is usually a developmental abnormality arising in the early prenatal period, typically failure of obliteration of the second, third, and fourth branchial cleft, i.e. failure of fusion of the second branchial arches and epicardial ridge in lower part of the neck. Branchial cleft cysts account for almost 20% of neck masses in children. Less commonly, the cysts can develop from the first, third, or fourth clefts, and their location and the location of associated fistulas differs accordingly. Most branchial cleft cysts present in late childhood or early adulthood as a solitary, painless mass, which went previously unnoticed, that has now become infected (typically after an upper respiratory tract infection). Fistulas, if present, are asymptomatic until infection arises. Branchial cleft cysts are remnants of embryonic development and result from a failure of obliteration of one of the branchial clefts, which are homologous to the structures in fish that develop into gills. The cyst wall is composed of squamous epithelium (90%), columnar cells with or without cilia, or a mixture of both, with lymphoid infiltrate, often with prominent germinal centers and few subcapsular lymph sinuses. The cyst is typically surrounded by lymphoid tissue that has attenuated or absent overlying epithelium due to inflammatory changes. The cyst may or may not contain granular and keratinaceous cellular debris. Cholesterol crystals may be found in the fluid extracted from a branchial cyst. The diagnosis of branchial cleft cysts is typically done clinically due to their relatively consistent location in the neck, typically anterior to the sternocleidomastoid muscle. For masses presenting in adulthood, the presumption should be a malignancy until proven otherwise, since carcinomas of the tonsil, tongue base and thyroid may all present as cystic masses of the neck.

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