Detecting serum-autoantibodies by anti-Desmoglein-1 (anti-Dsg1) and anti-Dsg3 ELISAs as well as indirect immunofluorescence (IIF) are established complementary methods to diagnose pemphigus. Whether autoantibody levels also reflect clinical disease activity is still a matter of debate, as head-to-head comparisons of ELISA values and IIF titres with clinical activity over a longer treatment period are scarce. In our retrospective study, we compared aggregated repetitive intra-patient ELISA values and IIF titres with grades of clinical disease (1 = remission, 2 = moderate activity, 3 = exacerbation) in 47 patients suffering from pemphigus vulgaris (PV, n = 36) and pemphigus foliaceus (PF, n=11). We found that anti-Dsg1 ELISA values in PF and mucocutaneous PV as well as anti-Dsg3 ELISA values in PV best reflect disease activity. IIF titres, by contrast, did not show a significant association with disease severity. From these data we conclude that ELISA index values can be a valuable tool to monitor disease in patients with pemphigus, whereas IIF titres reflect clinical activity only insufficiently.