Background <p>Type 1 diabetes mellitus (T1D) is a chronic autoimmune disease caused by the selective destruction of pancreatic beta cells, leading to insulin deficiency. Both genetic and environmental factors contribute to disease susceptibility. Among genetic factors, human leukocyte antigen (HLA) class II molecules, particulary DQA1 and DQB1 haplotypes, have been associated with T1D risk. This study aimed to identify haplotypes that increase susceptibility to or provide protection against T1D in Jordanian population.</p> Methods <p>A total of 200 healthy individuals and 200 T1D patients were included in the study. Genomic DNA was extracted from blood samples and HLA-DQA1, HLA-DQB1 and cytotoxic T-lymphocyte associated protein 4 (CTLA-4) gene regions were amplified by PCR. The PCR products were then subjected to restriction enzyme digestion and analyzed through agarose gel electrophoresis to determine different haplotypes.</p> Results <p>Among the analyzed haplotypes, HLA-DQA1*01:01 was found to be significantly associated with increased susceptibility to T1D. In contrast, HLA-DQA1*02:01 and HLA-DQB1*05:01 appeared to provide protective effects against T1D. No significant differences were observed for other haplotypes between the control and patient groups. Additionally, no significant difference has been observed in terms of CTLA-4 polymorphisms.</p> Conclusion <p>These findings suggest that HLA-DQA1*01:01 may serve as a genetic marker for T1D susceptibility, while HLA-DQA1*02:01 and HLA-DQB1*05:01 may confer protectionin the Jordanian population. Identifying these genetic risk factors could contribute to early disease prevention strategies and advanced research into additional genetic markers associated with T1D.</p>