Aim: The aim of this study was to examine the immunohistochemical expression of glypican-3 (GPC3) and enhancer of zeste homologue-2 (EZH2) in various histological types of hepatic nodules to investigate their discriminatory diagnostic value between primary malignant, metastatic and non malignant nodules. Materials and methods We correlated markers’ expression with the clinicopathological variables of primary liver malignancy. Markers’ expression was analyzed in 82 liver true-cut needle biopsies; 59.76% were primary liver malignancies, 15.85% were metastatic carcinomas, and 24.39% were nonmalignant nodules. Results GPC3 expression was detected in 84.37 and 17.64% of hepatocellular carcinomas (HCC) and cholangiocarcinomas (CC), respectively, but was not expressed in any of the metastatic nodules. In HCC, GPC3 was expressed more with cirrhosis, with large masses of tumor and with high HCC grades with statistically significant differences (P= 0.036, 0.024, and 0.030, respectively). EZH2 expression was detected in 90.62% of HCCs, in all cases of CC and metastatic nodules, and in 5% of nonmalignant nodules. The sensitivity, specificity, and diagnostic accuracy of differentiating HCCs from nonmalignant nodules were 84.38, 100, and 90.38%, respectively, for GPC3, and 90.63, 95, and 92.31%, respectively, for EZH2. The sensitivity, specificity, and diagnostic accuracy for differentiating HCCs from CCs were 84.38, 82.35, and 83.67%, respectively, for GPC3, and 90.63, 0.0, and 59.18%, respectively, for EZH2. The sensitivity, specificity, and diagnostic accuracy for differentiating HCCs from metastatic nodules were 84.38, 100, and 88.89%, respectively, for GPC3, and 90.63, 0.0, and 64.44%, respectively, for EZH2. Conclusion GPC3 can be used as a first-line marker for differential diagnoses of HCCs from nonmalignant nodules, CCs, and metastases (accuracy rate: 90.38, 83.67, and 88.89%, respectively). In HCC, overexpression of GPC3 is associated with poor prognostic factors such as large tumor size and high tumor grade. EZH2 is a reliable marker for HCCs compared with nonmalignant nodules (accuracy rate: 92.31%). However, EZH2 is not specific for HCC as all other examined hepatic malignancies were positive as well.