Autoimmune thyroid diseases (AITD), particularly Hashimoto's thyroiditis (HT) and Basedow-Graves disease (BGD) are diseases of global public health concern, characterized by autoimmune attacks on the thyroid gland, leading to hypothyroidism in HT and hyperthyroidism in BGD. We conducted a study between 2019 and 2021 in northwestern Transylvania (Romania) on patients with HT and with BGD compared to the control group. The aim of the study was to investigate the correlations of HLA class II alleles with AITD by identifying potential genetic susceptibility factors such as and genes in patients diagnosed with HT and BGD. Various molecular biology methods, including SSP-PCR low-resolution and PCR-SSO were employed to analyze DNA samples from patients and control subjects. Our study revealed the influence of the genotype as a genetic susceptibility factor for HT, a similar influence regarding BGD being observed for the allele group, genotype, and the haplotype. The only protective factor detected in our study was the allele group, for both HT and BGD. By elucidating any specific allele or genotype associations that might contribute to the development of AITD, our study can contribute to the prevention and early detection of these diseases.