BackgroundBasaloid squamous cell carcinoma (BSCC) is a rare subtype of squamous cell carcinoma with a high rate of distant metastasis. BSCC occurs most commonly in the esophagus, lungs, and head and neck. However, BSCC occurring in an atypical site without a known primary tumor and/or with the presence of atypical immunohistochemical features can result in delayed diagnosis or misdiagnosis.Case presentationHere, we report a case of a 67-year-old man with liver metastatic BSCC with negative pancytokeratin (AE1/AE3) expression. He presented with a chief complaint of epigastric discomfort. Imaging examination revealed a subcapsular mass in the right anterior lobe of the liver. Then, the patient underwent an irregular right hepatectomy. Grossly, the mass was gray, with a size of 7 × 7 × 4 cm. Microscopically, the mass comprised epithelioid tumor cells with both solid and pseudoadenoid structures, accompanied by necrosis. Immunohistochemical staining showed that the tumor cells were negative for AE1/AE3, CK18, CK7, CK19, Hepatocyte Paraffin-1, Glypican-3, Arginase-1, CD56, Chromogranin A, Synaptophysin, Vimentin, and Carcinoembryonic antigen. The Ki-67 index was 80%.The mass was diagnosed as a malignant tumor but could not be classified further. One month after surgery, the patient’s reexamination revealed esophageal tumor, and biopsy revealed BSCC. The slides of the liver tumor were reviewed, and the morphology was similar to that of the esophageal tumor. Moreover, supplementary immunohistochemical staining of liver tumor indicated p63 and p40 were strongly positive, that confirmed the liver tumor was metastatic BSCC. Previous studies have reported that 3.7% of esophageal BSCCs did not express AE1/AE3.ConclusionWhen a malignant tumor comprises epithelioid cells with solid and/or pseudoadenoid structures, but not adenocarcinoma or neuroendocrine carcinoma, even if the tumor cells are negative or weakly positive for AE1/AE3, we should consider BSCC. For a definite diagnosis, immunohistochemical staining for squamous cell carcinoma markers, including p63 and p40, and examination of common primary sites of BSCC should be performed.