Background: Previous reports have shown that indirect immunofluorescence (IIF) performed on sodium chloride-split skin (SSS) is helpful to differentiate epidermolysis bullosa acquisita (EBA) from bullous pemphigoid (BP). Antibodies of BP may bind to the epidermal side of SSS, while antibodies of EBA bind to the dermal side. Aims: To determine the accuracy of IIF-SSS in the differential diagnosis of EBA and BP utilizing immunoblotting (IB) analysis. Methods: Sera from 78 patients, diagnosed with BP by clinical features, histopathology, and direct immunofluorescence (DIF), were assayed using IIF-SSS and IB. Results: Of the 43 serum samples with an epidermal reaction to IIF-SSS assay, 42 were recognized with BP antigens (180 kDa or 230 kDa). Of the 11 serum samples with a dermal reaction pattern, 7 were recognized with the 290 kDa antigen of EBA and 3 with sera bound BP antigens. Seven serum samples with epidermal and dermal combined staining, of which 5 of them reacted with BP antigens, 1 reacted with both BP and EBA antigens. One serum sample from each group showed a negative result by IB. Approximately 9.0% (7/78) of patients diagnosed with BP using regular methods were actually EBA. Conclusions: Epidermal reaction using the IIF-SSS assay highly correlated with the diagnosis of BP. However, dermal reactions correlated poorly with EBA, with some serum samples from BP patients binding to dermal-side antigens. In both epidermal and dermal stained sera using IIF-SSS, there was a possibility of BP and EBA. Differential diagnosis should be confirmed using IB, especially in cases of dermal and double staining patterns assayed using IIF-SSS.