Objective: 1) Describe the diagnostic dilemma of finding a thyroid carcinoma in a lateral neck mass without a primary. 2) Understand the etiological theories of branchial cleft cysts. 3) Be able to manage a patient with thyroid carcinoma in a lateral neck mass without a primary site identified. Method: We report a rare case of papillary thyroid carcinoma incidentally found within a branchial cleft cyst. Only 4 other cases have been described in the literature. A total thyroidectomy and selective neck dissection was performed and no evidence of occult primary disease was found after review of fine sections. Results: Branchial cleft cysts are the most common lateral neck masses. Ectopic thyroid tissue within a branchial cleft cyst is an unusual phenomenon and papillary thyroid carcinoma arising from this tissue is extremely rare. Clinicians are left with a diagnostic dilemma when presented with thyroid tissue neoplasm within a neck cyst in the absence of a thyroid primary—is this a case of metastatic disease with a missed primary or rather carcinoma arising in ectopic thyroid tissue? A thorough discussion of the etiologies of these lateral neck masses is reviewed including the embryogenesis of thyroid tissue in a branchial cleft cyst. Conclusion: The prognosis of patients with papillary thyroid carcinoma in lateral neck cysts without a primary site identified appears to be good following excision of the cyst and total thyroidectomy. Other management recommendations regarding these unique lateral neck malignancies are also presented.