Background: Malignant pleural mesothelioma (MPM) is a fatal tumor that originate from the mesothelial cells. Sometimes, it is difficult to be diagnosed based on morphology alone as reactive mesothelial hyperplasia (RMH) and some metastatic carcinomas may be confused with mesothelioma. Our study aims to adjust diagnostic value of BRCA1 “Breast Cancer gene” associated protein-1 (BAP1), Programmed Cell Death4 (PCD4), and Epithelial membrane antigen (EMA) in differentiation of malignant mesothelioma (MM) from reactive mesothelial hyperplasia (RMH) by immunohistochemistry (IHC). Methods: This retrospective study, include 60 patients, was carried out in Chest and Pathology Departments of Zagazig University from October 2016 till August 2020. The expression levels of BAP1, PCD4 and EMA were investigated using cytological analysis compared with cell block method in all cases of MPMs and RMH. Results: BAP1loss was detected in cases of malignant mesothelioma confirmed by cytology in 19 out of 20 patients with sensitivity of 95%, specificity 92.5%. PCD4 was positive in 39 out of 40 patients of RMH and can diagnose reactive mesothelioma with sensitivity of 85.7% and specificity 100%. EMA was positive 95% in MM confirmed by cytology and can diagnose malignant mesothelioma with a sensitivity of 95% and specificity 97.5%. Conclusions: Cell block method increases the sensitivity of diagnosis in cases that were recorded as reactive mesothelial hyperplasia by conventional cytological smears. BAP1 loss, negative PCD4 and positive EMA immunostaining can differentiate and diagnose MM from RMH with improved diagnostic accuracy.