Lymphoepithelial cysts with histological features characteristic of branchial cleft cysts have been reported to occur rarely in the thyroid gland. To our knowledge only six cases of this lesion have been reported. Since these reports brought this entity to our attention, we have noted that intrathyroidal lymphoepithelial cysts are not rare lesions. We report six further cases; four were incidental histological findings, and two lesions were clinically detected masses. Each of the cysts had a squamous epithelial lining with abundant underlying lymphoid tissue, including lymphoid aggregates with large reactive germinal centers. All cases were associated with chronic lymphocytic thyroiditis. Because of the histological resemblance to branchial cleft cysts, it is postulated that these lymphoepithelial cysts are branchial in origin. The histogenesis of branchial cleft cysts is unknown; however, the ultimobranchial body, originating from branchial pouches four and/or five, contributes to the embryological development of the thyroid. Branchial cleft derivatives, such as thymus and parathyroid, develop in close association with the thyroid and may be found within the thyroid gland. These branchial cleft-like cysts also may arise from branchial cleft derivatives, and their enlargement may be related to the immunological mechanisms associated with autoimmune thyroiditis.