Autoimmune thyroid diseases (AITDs), including Graves' disease (GD) and Hashimoto's thyroiditis (HT), represent the most common organ-specific autoimmune disorders worldwide. Their development results from a complex interaction between genetic susceptibility and environmental triggers. Among genetic determinants, human leukocyte antigen (HLA) genes located within the major histocompatibility complex (MHC) are of primary importance. Specific HLA class II polymorphisms influence antigen presentation, T-cell activation, and tolerance breakdown. This article reviews the immunogenetic basis of AITD with emphasis on HLA structure, functional polymorphisms, molecular mechanisms of susceptibility, and available population data, highlighting the need for further investigation in the Albanian population.