The M-type phospholipase A2 receptor (PLA2R1) was identified recently as a specific target antigen in idiopathic membranous nephropathy. However, the influence of different sample preparation techniques on the immunostaining of PLA2R1 is unclear. Previous studies have identified IgG4 as the dominant subclass of PLA2R1 antibodies. However, it remains unclear whether the IgG subclass profiles of the glomerular immune complexes of PLA2R1-positive and -negative idiopathic membranous nephropathy cases are similar. To address these questions, we conducted the present study of 58 idiopathic membranous nephropathy cases. The PLA2R1 positivity rate for the paraffin-embedded sections was 61%, whereas that for the frozen sections was 65%. Nonspecific background staining was observed in the frozen sections. Discrepancies between different sample preparations occurred in three cases (6%); two cases were PLA2R1-positive in paraffin sections and PLA2R1-negative in frozen sections and one case was PLA2R1-negative in paraffin sections and PLA2R1-positive in frozen sections. Regarding the IgG subclass profile, 89% of the PLA2R1-positive cases demonstrated the IgG4-dominant/codominant phenotype versus 31% of the PLA2R1-negative cases (p < 0.001). Clinical characteristics and pathological findings did not significantly differ between PLA2R1-positive and -negative cases. In summary, the PLA2R1 immunofluorescence results were not affected by the different sample preparation techniques, although paraffin-embedded sections were preferred for the histological detection of PLA2R1 because of the nonspecific background staining observed in frozen sections. The observed lower frequency of the non-IgG4-dominant/codominant phenotype in PLA2R1-negative idiopathic membranous nephropathy cases may suggest that there are heterogeneous subgroups of this disease.