Type1 Diabetes Mellitus (TIDM) is an autoimmune disease characterized by absolute insulin deficiency resulting from cellular-mediated and humeral autoimmune destruction of islet beta cells. This study was carried out to investigate the possible association of human leukocyte antigen (HLA) class I and II alleles with T1DM using pcr-sso and the possible association between HLA and autoantibodies (GADA,IA-2 and ICA). Seventy type 1 Diabetes Mellitus with age range (1-30 years) a mean of (9.52) were enrolled in this study, they were attended AL-Escan hospital for children , AL-Kadhumyia Teaching Hospital in addition on 30 appearantly healthy individual gender matched with the patient, During the period of November/2010 to May/2011. Autoantibodies of GADA & IA-2A were detected by using Enzyme Linked Immunosorbant Assay(ELISA technique) and for ICA, Indirect Immunofluorescence (IIF) was used. In order to investigate the association between HLA and T1DM and any relation between HLA with ICA,GADA &IA-2, genotyping by Polymerase Chain Reaction-Sequence Specific Oligonucleotide Probes (PCR-SSOP) technique was done for patients as well as for control group in this regard. From the current study it was noticed: Among HLA-DQ alleles, DQB1*0101 and DQB1*0201 (9.28% vs.zero %) with OR of 12.8 respectively (P= 0.001), showed highly significant association with T1 DM in comparison with healthy control. These two alleles might be considered as a risk factor in T1DM. While these was significant low frequency of HLA- HLA-A*3301, B*0826 , DRB1*0701, *1101 and HLA-DQB1-*0604 alleles in TIDM in comparison with healthy control suggesting that these alleles may confer protective effects against disease. Concerning Islet Cell Antibodies (ICA) , Glutamic Acid Decarboxylase (GADA) and IA-2 the results showed statically a significant difference (p<0.05) in the seropositivity of DM patients in comparison with control group (ICA 32.25% , GADA 80% IA-2A 44.07%). In addition, there is no association between HLA-A and HLA-B alleles with the presence of autoantibodies. On the other hand the current findings observed that HLA-DR*1103 alleles negative associated with IA-2A (p=<0.001), while there was negative significant association between HLA-DR * 1303 and GADA (P= 0.038). As well as the present study showed that HLA-DQ*0101,*0309, *0501 and 0204 alleles significantly negative associated with IA-2A these alleles may play a role as protective factors (p=0.002, 0.020, 0.035, 0.002).