Pemphigus is a group of autoimmune blistering diseases of which the major forms are pemphigus foliaceus (PF) and vulgaris (PV). In Brazil, PF occurs in an endemic form also known as fogo selvagem. The main autoantibody in PF is against desmoglein 1 (DSG1), while in PV the main antibody is anti-desmoglein 3 (DSG3), but often anti-DSG1 is also present. The aim of the present study was to analyze the levels of anti-DSG1 and antiDSG3 autoantibodies in Brazilian PF and PV patients, considering different stages of the disease for PF patients and comparing these levels to those of healthy individuals living in and outside the endemic regions. Levels of anti-DSG1 and anti-DSG3 were measured in the sera of Brazilian PF (n = 68) and PV (n = 20) patients as well as in clinically healthy (control) individuals (n = 48) by Enzyme Linked Immunosorbent Assay (ELISA). Comparisons were made using Kruskal-Wallis and Mann-Whitney tests. As expected, anti-DSG1 was more prevalent among PF patients (84% against 43% in PV), while antiDSG3 was more prevalent in PV patients (50% against 4% in PF). Levels of anti-DSG1 in PF patients in remission differed from those in patients undergoing active disease (p = 0.003), and patients in long-term remission (more than two years without presenting new lesions) were similar to control individuals living in the endemic region and surrounding area (p = 0.09). Moreover, patients with a more severe form of the disease had higher levels of anti-DSG1 (at least 134 U/mL, mean of 233 U/mL) than patients with a less severe form (fewer lesions) (mean of 193 U/mL, including two negative individuals). Despite the importance of these antibodies for diagnosis and management purposes, their presence in a healthy individual and in patients under remission indicates that caution should be taken when using anti-DSG for diagnosis, especially in endemic areas.