Cyst fluid was aspirated from five thyroglossal duct cysts (TDCs) and four branchial cleft cysts (BCCs). The cyst fluid levels of carcinoembryonic antigen (CEA), carbohydrate antigen (CA) 19-9, squamous cell carcinoma antigen (SCC), and amylase were measured and compared between the two types of cyst. The enzyme immunoassay technique was used for CEA and CA19-9, while SCC and amylase levels were measured by the immunoradiometric assay and nitrophenol method, respectively. Immunostaining for CEA, CA19-9, and amylase was also performed. The serum levels of these markers in both groups of patients were within the normal ranges. In contrast, their cyst fluid levels were extremely high. There was no significant difference in the cyst fluid levels of CEA and SCC between the two types of cyst; however, the cyst fluid from the TDCs showed significantly higher levels of CA19-9 and significantly lower levels of amylase compared with that from the BCCs. Immunostaining revealed expression of CA 19-9 in nearly half the columnar epithelial cells in the TDCs, but not in the squamous epithelial cells in the BCCs. CEA and amylase were not found in the epithelial cells of either type of cyst. These findings seem to reflect the difference in etiology between TDCs and BCCs.