Autoimmune thyroid diseases (ATD), including Hashimoto’s thyroiditis and Graves’ disease, are among the most common autoimmune disorders and arise from complex interactions between genetic susceptibility and environmental factors. The human leukocyte antigen (HLA) region on chromosome 6p21 plays a major role in immune regulation and disease susceptibility. However, the distribution of HLA alleles varies across populations, and data from Balkan populations remain limited. This study aimed to investigate the distribution of HLA class I and class II alleles in Albanian patients with autoimmune thyroid disease.