Distinguishing primary from secondary forms of membranous nephropathy (MN) in paraffin-embedded kidney biopsies is challenging. Previous studies have measured the accuracy, sensitivity, and specificity of phospholipase A2 receptor (PLA2R) on MN. However, due to the absence of a gold standard method for diagnosis, further studies are necessary. Here, we measure the correlation and discrepancy of PLA2R on MN in paraffin-embedded kidney biopsies by correlating PLA2R findings with immunofluorescence (IF), light microscopy (LM), and electron microscopy (EM) results. A total of 116 kidney biopsies were investigated including 87 MN and 29 nonmembranous kidney diseases. PLA2R was examined by indirect IF assay. A total of 79 MN cases were subjected to PLA2R staining and histopathological analyses. The remaining eight cases were excluded due to the lack of the glomeruli in the sections. The correlation and discrepancy between PLA2R and IF findings were seen in 65.45% and 34.55%, respectively. PLA2R and EM findings showed a 65.52% correlation and 34.48% discrepancy. LM features and PLA2R findings showed a correlation of 58.44% and discrepancy of 41.56%. Overall correlation between histopathology and PLA2R was seen in 65.82% and 34.18% showed discordant cases. All 29 non-membranous MN cases were negative for PLA2R. Staining for PLA2R could be a useful adjunctive tool in the stratification of cases of MN. The findings of this study strongly recommend the use of PLA2R IF staining method as a routine test for all MN cases.