Malignant cyst of the lateral aspect of the neck: branchial cleft carcinoma or metastasis? A 58-year-old man had a left jugulodigastric mass, which was found to be cystic by computed tomography, and no evidence of other lesions. Grossly and histologically, the surgical specimen consisted of a thin-walled, fluid-filled cyst lined by squamous epithelium that varied in appearance from benign to invasive squamous cell carcinoma. The findings supported a differential diagnosis of branchial cleft carcinoma (BCCA) versus cystic growth of a lymph node metastasis from an occult malignancy. On this basis, guided biopsies of the upper aerodigestive tract were performed, with strong suspicion of a tonsillar bed lesion. Microscopic examination revealed the primary tumor within tissue excised from the left tonsillar fossa. Comparison of the current case with cases of BCCA and cystic tonsillar metastases from the literature illustrated the potential pitfalls in rendering a diagnosis of BCCA. Recognition of this lesion as a distinctive clinical variant of oropharyngeal carcinoma is warranted. 