HLA-DQA1 encodes the alpha chain of MHC class II molecules, which present exogenous peptide antigens (10-30 residues) to CD4+ T cells on antigen-presenting cells 1. The protein functions as part of a heterodimeric complex that binds peptides processed through the endosomal-lysosomal pathway after CD74-mediated loading and CLIP removal facilitated by HLA-DM 2. HLA-DQA1 allelic variants are strongly associated with multiple autoimmune diseases through altered peptide presentation. Specific alleles confer disease risk: DQA1*03:01 and *01:01 increase type 1 diabetes (T1D) susceptibility 34, while DQA1*02:01 provides protective effects in Jordanian T1D populations 4. Similarly, HLA-DQA1*0301 increases Vogt-Koyanagi-Harada disease risk, whereas DQA1*0103, *0401, and *0501 are protective 2. Clinically, HLA-DQA1 polymorphisms influence therapeutic responses. The DQA1*05 allele increased immunogenicity to anti-TNF drugs but did not affect response to ustekinumab or vedolizumab in inflammatory bowel disease 5. HLA-DQA1 variations (rs9272346) were not significantly associated with glatiramer acetate resistance in multiple sclerosis 67. These findings suggest HLA-DQA1 genotyping may facilitate personalized risk stratification and treatment selection in autoimmune conditions.