Type1 diabetes (T1D) and celiac disease (CD) may occur together. HLA-DQ8 and DQ2 are key genetic risk factors in both. Overall, the patients with co-existing T1D and CD (T1D+CD) were shown to have HLA profile more similar to patients with T1D than those with CD. Slovenian patients with both diseases had the frequency of DQB102:01 (86.5%) very similar to patients with CD (83.8%) in contrast to the significantly different frequency of the same allele in patients with T1D (52.24%). The DQ2 conveyed higher risk for developing both T1D and CD in the same individual than DQ8. Additionally, the A1-B8-DR3-DQ2-MICA008 ancestral haplotype (8.1AH) was over-represented in Slovenian (T1D+CD) patients, where B08 was the most significant independent risk factor. Moreover, C07, that is also present in the 8.1AH, could have an impact on the innate immunity rout of this susceptibility through interaction with KIRs. In the genotype context, the CD risk in T1D patients was associated with DR3-DQ2/DR3-DQ2, whereas the risk for T1D in CD patients was associated with DR3-DQ2/DR4-DQ8. Less frequent screening for the second disease related antibodies could be considered in patients with the first disease and low risk genotype for obtaining the second-one. Individuals carrying high risk DR3-DQ2/DR3-DQ2 or DR3-DQ2/DR4DQ8 are more likely to develop both autoimmune diseases together than individuals carrying any other HLA genotypes.