Pemphigus vulgaris (PV) is an autoimmune disease involving the skin and mucous membranes. The frequency of upper airway tract (UAT) and upper gastrointestinal tract (UGIT) involvement in PV is not clearly known. Our aim was to determine the incidence of UAT and UGIT involvement in patients with PV. Thirty-seven patients who were diagnosed with PV and treated between March 2008 and April 2009 at the Dermatology Department of the Vakif Gureba Teaching and Research Hospital were included. All patients were evaluated for UAT manifestations by endoscopic examination, and 22 of 37 patients were investigated for UGIT involvement by gastrointestinal endoscopy. Mucosal biopsies were obtained by UGIT endoscopy for direct immunofluorescence (DIF) examination, and a histopathological examination was conducted in patients with active UGIT mucosal lesions. Thirty-five of 37 patients (94.6%) had active pharyngeal, laryngeal, or nasal PV lesions on endoscopic evaluation. Oral symptoms (83.8%) and active oral PV lesions were the most frequent findings (100%). Pharyngeal lesions (64.9%) were the most commonly present lesions on UAT examination. The frequency for laryngeal and nasal lesions was 51.4% and 21.6%, respectively. Five of 22 patients (22.7%) presented with active laryngeal and esophageal lesions. Twenty-one of 22 (95.4%) patients had positive DIF results. We believe that UAT and UGIT endoscopies are useful and necessary diagnostic methods in patients with PV with or without UAT and UGIT symptoms. UAT and UGIT endoscopies should be performed as standard diagnostic procedures in all patients with PV.