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Carcinoembryonic antigen (CEA) is a widely used, non-specific tumour marker for gastrointestinal (GI) malignancies, particularly colorectal cancer (CRC). However, it can also be elevated in non-GI tumours and benign conditions, which are often overlooked. A 60-year-old, asymptomatic man was referred for assessment of GI malignancy. During a health screening check, he was found to have a markedly elevated CEA, 121.8 ng/mL (reference range: <5.0 ng/mL). His family history included CRC, breast, and thyroid cancers. GI evaluation, which included a colonoscopy and gastroscopy, identified only a small sigmoid polyp and <i>Helicobacter pylori</i> gastritis. A pan-computed tomography (CT) scan showed a left thyroid nodule. He had fine-needle aspiration biopsies of the thyroid nodule on two occasions, and both were negative for malignancy. Serum calcitonin was markedly elevated. Following a discussion, the patient underwent total thyroidectomy, which confirmed multifocal medullary thyroid carcinoma (MTC). Postoperatively, the serum CEA declined and normalised after four months. Genetic testing revealed a germline RET mutation, establishing hereditary MTC. CEA elevation is commonly evaluated for GI malignancies. This case report highlights that MTC is also associated with elevated CEA. Therefore, this should be assessed when GI evaluations are negative, to avoid delay in diagnosis.