To study the clinicopathological features of malignant transformation of the epithelial component of a Warthin tumour into adenocarcinoma. The histological and immunophenotypic features of the malignant transformation of the epithelial component of a Warthin tumour into adenocarcinoma were studied, and the literature was reviewed. The patient had a history of surgery for a Warthin tumour 3 years previously, and the typical histological manifestations of a Warthin tumour were observed under the microscope following biopsy. Scattered tumour tissue infiltration was observed in the lymphatic interstitium, and a transitional area of benign and malignant epithelial cells was observed locally. The tumour cells were solid, nested, and glandular and grew infiltratively in the salivary gland tissue. There was diffuse positive staining for CK7 and CK19 in the cytoplasm of tumour cells. CK5/6 was positively expressed in the cytoplasm of basal cells in the tumour tissue, and P63 was positively expressed in the basal cell nuclei. Ki-67 positivity reached approximately 10% in tumour tissues. The MAML2 fracture probe result was negative. The final diagnosis was malignant transformation of a Warthin tumour, with malignant transformation of epithelial components into adenocarcinoma. Malignant transformation of a Warthin tumour is rare, and the intraoperative histopathological diagnosis based on frozen sectioning should be made with caution. The key to diagnosis is to determine whether there is migration between benign and malignant epithelium.