In this study, we used whole genome sequencing data from two Hungarian families affected by CD to analyze the HLA-related genetic mechanisms behind it. We used bash scripting to run an open-source genotyping algorithm to predict the alleles of the different HLA genetic regions. After this, we extracted, analyzed, and compared the haplotype frequencies in CD-affected individuals against non-affected ones. We found that, in line with previous findings, the HLADQ2.5 haplotype was predominant in our study group, and there was almost no evidence of the HLADQ8 haplotype. Using descriptive statistics methods, we found evidence of a strong linkage disequilibrium factor in our population. Affected individuals might be carrying the ancestral haplotype AH 8.1, composed of HLA-A1, Cw7, B8, DRB10301, DRB30101, DQA10501, and DQB10201 alleles.