Background Pemphigus vulgaris (PV) is a chronic progressive autoimmune bullous disease caused by the interaction of pathogenic factors, genetic, and environmental factors. HLA alleles, which are considered as protective factors against disease or predisposing factors, may be different in various populations and ethnic groups. Aims The purpose of this study is to examine the HLA-A, HLA-DR, and HLA-DQ alleles in patients that are diagnosed with PV in and around eastern of Turkey and to determine the alleles that create predisposition to disease or protect against the disease. Patients/Methods Thirty patients diagnosed as PV with clinical, histopathological, and immunofluorescence findings and 30 healthy subjects were included in this study. The HLA-A, HLA-DR, and HLA-DQ typology in the DNA samples that were obtained from the blood samples of the groups was performed by using the PCR-SSP low-resolution gene panels. Results The HLA-A*03 allele was found to be significantly higher in patient group than the control group (P-value: .020). HLA-DRB1*04 and HLA-DRB1*14 alleles in PV patients were found to be significantly higher than the control group (P-value = .000). Conclusion It was concluded that the HLA-DRB1*03, HLADQB1*02, and HLA-DQB1*06 alleles in and around eastern of Turkey showed protective effects against pemphigus vulgaris. It was also concluded that the HLA-A*03, HLA-DRB1*04, HLA-DRB1*14, HLA-DRB4, HLA-DQB1*03, and HLA-DQB1*05 alleles could cause predisposition to the disease.