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Aims - To describe the clinical features, epidemiology, autoantibody status, HLA haplotypes and genetic mechanisms of type 1 diabetes mellitus (T1DM). Methods - Patients (0–18 years) with diabetes were recruited. Clinical data was collected, autoantibodies and c-peptide were measured. Whole Genome Sequencing was performed. Genomic data analysis was compared with the known genes linked with T1DM and HLA alleles were studied. Results - 1096 patients had one or more antibody positivity. The incidence of T1DM in 2020 was 38.05 per 100,000 children and prevalence was 249.73. GAD65 was the most common autoantibody and IA2 was most specific. Variants in GSTCD, SKAP2, SLC9B1, BANK1 were most prevalent. An association of HLA haplotypes DQA1*03:01:01G (OR = 2.46, pvalue = 0.011) and DQB1*03:02:01G (OR = 2.43, p value = 0.022) was identified. Conclusions - In this first prospective study, IA2 autoantibody was the most specific, some patients only have ZnT8 or IA2 autoantibodies thus underlining the necessity of profiling all 4 antibodies. The genes associated with T1DM in the Arab population were different from those that are common in the Caucasian population. HLA-DQ was enriched in the Qatari patients suggesting that it can be considered a major risk factor at an early age.