Celiac disease (CD) is an autoimmune enteropathy triggered by ingestion of gluten present in wheat, barley, and rye. Gluten along with environmental trigger starts an inflammatory reaction which results in damage to small intestine. Human leukocyte antigen (HLA)-DQA1∗05, -DQB1∗02, and -DQB1∗03:02 are the known risk alleles of CD. The diagnostic method for CD involves serological or intestinal biopsy, but genetic test could be implemented. HLA typing precludes the need for further diagnosis and it has high negative predictive value. The aim of this study was to make aware of HLA molecular typing for celiac disease among local laboratories and healthcare professionals. The prevalence and frequency distribution of HLA-DQ2 and -DQ8 haplotypes in 175 pediatric unrelated healthy controls, celiac patients, and CD with concurrent diabetes mellitus type 1 (DM1) was evaluated. The most common haplotype was DQ2 followed by DQ8. In control group only DQ2 was observed with frequency of 8.5%. In celiac patients 85.7% were DQ2, 11.4% were DQ8, and rest were DQ2/DQ8 (2.8%), and all had CD. In the group of CD with DM1, 31.4% had DQ2, 25% had DQ8, and 34% having both the haplotypes; while only 9 of these patients were suffering from CD. It was concluded that Celiac disease is frequently unrecognized by physicians, in part because of its variable clinical presentation and symptoms. Thus genetic testing for celiac disease could be an additive tool for diagnosis to exclude ambiguity.