Background Pemphigus is an autoimmune blistering disease affecting the skin and mucosa, which mostly in anecdotal reports has been associated with several autoimmune diseases. Objective The aim of this study was to assess the frequency of autoimmune diseases in a large group of patients with pemphigus and their first-degree relatives. Methods One hundred and ten patients with pemphigus were interviewed for the existence of various autoimmune diseases. Patients' sera were examined for the presence of several autoantibodies. The existence of autoimmune diseases in 969 first-degree relatives of the patients was assessed via questionnaires. Results Seven of 110 (6.3%) patients with pemphigus had concurrent autoimmune diseases, including four (3.6%) with autoimmune thyroid disease and three (2.7%) with rheumatoid arthritis. Ten of 969 (1.03%) first-degree relatives of patients with pemphigus had autoimmune thyroid disease, three (0.31%) had rheumatoid arthritis, and three (0.31%) had type 1 diabetes mellitus. The patient's group had a statistically significant higher prevalence of thyroid disease and rheumatoid arthritis than their first-degree relatives (P=0.046 and 0.016 respectively). Conclusions Patients with pemphigus seem to have a higher rate of autoimmune thyroid disease and rheumatoid arthritis than both the general population and their own first-degree relatives. Further studies comparing patients with pemphigus with healthy controls are needed to stratify their risk factors for developing other autoimmune diseases and to define guidelines regarding diagnosis and treatment of coexistent autoimmune disorders.