Background: Celiac disease (CD), considered as a common chronic and genetic disease that caused by hypersensitivity to gluten. Failure to thrive (FTT), is one of three major clinical features of CD during childhood. Objectives: The current study aimed to determine the frequency of celiac disease in children with malnutrition. To assess and compare the HLA geno typing of those has positive serology for celiac disease with other studies. Patients and Methods: one hundered malnourished children (52 males, 48 females), age ranged between 6-60 months with the diagnosis of malnutrition according to WHO criteria who were currently attending the Rehabilitation Unit of Malnutrition at a Child’s Central Teaching Hospital in Baghdad city during 13 months and from begging of September 2016 to end of September 2017, All patients were screened for CD using the IgA and IgGantitissuetransglutaminase antibody test(tTG). HLA typing was performed in patients with positive IgA and IgG-tTG serology. A comparison was made between celiac and nonceliac according to age, gender, chief complain, clinical feature, residence, onset of complementary feeding and type of feeding. Results: eleven of 100 malnourished patients (11%) had positive tTG antibodies, 8 ( 72.7%) patients were males and 3 (27.2%) were females, Among these 11 patients,(4) were only tTG IgA positive, one only tTGIgG positive and 6 positive for both (IgA, IgG) with male to female ratio 2.6:1, 90.9% of celiac patients carry DQ2, (27.3%) carry DQ8 and (18.1%) carry both DQ2 and DQ8. It was found that celiac disease were significantly higher at age group (37-60 months) and in those who had started early complementary feeding, abdominal distention and diarrhea were higher in celiac patients Conclusion: At current study, the prevalence of CD in children with malnutrition was 11%.HLA typing was comparable to that of other studies. Since CD is an important cause of malnutrition in children, tTG and HLA typing is available tool that can be used for screening celiac disease at an earlier age.