Pemphigus is an autoimmune blistering disease of the skin and mucous membranes caused by autoantibodies against desmoglein 1 (Dsg1) and desmoglein 3 (Dsg3). Pemphigus vulgaris (PV) is the most common form of pemphigus. The aim of this study was to assess the correlation between the levels of anti-desmoglein 1 and 3 autoantibodies and the severity of PV disease. Nineteen newly diagnosed patients with pemphigus vulgaris were enrolled in this study. The titers of Dsg in subjects by using enzyme-linked immunosorbent assay (ELISA) were done at diagnosis time-point, 4th and 8th weeks after the initiation of treatment, and the correlation of antibodies with the oral and skin disease severity was evaluated. The severity of cutaneous lesions was significantly correlated with anti-Dsg1 titer in all visits and the severity of mucosal lesions was correlated with the titer of Dsg3 in the third visit (<0.001, 0.001, 0.016 and 0.015 P value, respectively). Anti-Dsg-1 autoantibodies titers seem to be more useful in showing the extent of the disease and activity in pemphigus with mucocutaneous lesions.