OBJECTIVE: This study aimed to develop a reproducible immunohistochemistry method for formalin-fixed, paraffin-embedded (FFPE) muscle sections and to assess its diagnostic utility for idiopathic inflammatory myopathies (IIM) in settings where snap-frozen muscle biopsy is unavailable. METHODS: Twenty cases were analysed: dermatomyositis (n = 5), inclusion body myositis (n = 2), immune-mediated necrotizing myopathy (n = 5), overlap myositis (n = 1), unspecified myopathy (n = 3), mitochondrial myopathy (n = 1), LGMD R2 dysferlin-related muscular dystrophy (n = 1), facioscapulohumeral muscular dystrophy (n = 1), and neurogenic muscle change (n = 1). Immunohistochemistry was performed on 3-μm FFPE muscle sections using heat-induced antigen retrieval with citrate/EDTA buffer and overnight incubation at 4°C with antibodies against MHC-I, MHC-II, MAC, MxA, and p62. Frozen sections were analysed in parallel for comparison. RESULTS: Comparable staining intensities and patterns for MHC-II, MxA, and p62 were achieved in FFPE muscle sections. Although discrepancies between frozen and FFPE sections occurred in eight cases, each involving a single marker, no statistically significant differences in immunohistochemical results were observed for MHC-II (P = 0.4795), MxA (P = 0.4795), and p62 (P = 0.6171). Concordance between methods was high, reaching 90% for MHC-II and MxA and 80% for p62. These isolated discrepancies may reflect variability in antigen expression associated with the segmental and patchy involvement characteristic of IIM. However, MHC-I and MAC staining were unsuccessful in FFPE sections. CONCLUSIONS: Successful immunolabelling of MHC-II, MxA, and p62 was achieved in FFPE muscle sections. These findings indicate that several diagnostically informative markers for IIM can be reliably assessed in FFPE muscle, providing a practical diagnostic option in resource-constrained settings.