免疫組織化學染色在肝臟腫瘤的評估上經常扮演重要的角色。現行的分類系統將肝細胞腺瘤(hepatocellular adenoma)分為四類，可用免疫組織化學染色的結果搭配組織型態學和分子特性來區分。肝臟型脂肪酸結合蛋白(liver fatty acid binding protein, LFABP)在HNF1α不活化型肝細胞腺瘤會喪失表現，血清澱粉狀蛋白A(serum amyloid A, SAA)在發炎型肝細胞腺瘤會呈陽性染色，麩醯胺酸合成酶(glutamine synthetase, GS)則會在β-catenin活化型肝細胞腺瘤呈廣泛陽性染色。使用磷脂肌醇蛋白聚糖3(glypican-3, GPC-3)、熱休克蛋白70(heat shock protein 70,HSP70)和麩醯胺酸合成酶(GS)三項免疫組織化學染色的組合也可協助區分肝細胞癌及分化不良結節(dysplastic nodule)。在需要辨別肝臟原發或轉移的腫瘤時，磷脂肌醇蛋白聚糖3(GPC3)、精氨酸酶1(arginase-1, ARG-1)和膽鹽輸出幫浦(bile salt export pump, BSEP)等免疫染色亦可提供幫助。

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