Pemphigus is a rare autoimmune life-threatening blistering condition affecting skin and mucous membranes. Pemphigus belongs to a family of polygenic disorders. Several different genes encoding molecules regulate pemphigus autoimmunity. Many trials focused on HLA investigation. Increased levels of certain HLA class II alleles frequencies in pemphigus have been reported in various populations. However, they were not investigated in the Russian population. The aim of our study is to investigate HLA class II alleles and haplotypes in Russian patients with pemphigus. Methods Patients and controls We are recruiting 120 patients with pemphigus. The diagnosis was based on clinical and histopathological findings and confirmed by immunofluorescent techniques (direct and indirect immunofluorescent tests). Before sampling, written consent was obtained from each subject. A single blood sample for HLA typing was obtained from all subjects. This study has been approved by the Ethics Committee of Sechenov University, Russia. Phenotypic and allelic frequencies were compared with healthy blood donors (n=100) registered in Sechenov University blood center.