Background. We aimed to investigate the relationship between human leukocyte antigens (HLA)-groups andclinical features, and degree of intestinal injury in children with celiac disease (CD).Methods. Study group included 73 (50 females, 68.5%) children with CD. Demographic and clinical features,accompanying autoimmune diseases, family history for CD and degree of damage in small intestinal mucosa(according to Marsh classification) at the time of diagnosis were determined. Twenty-two siblings of celiacpatients without CD (15 females, 65.2%) consisted control group 1, and 66 (40 females, 60.6%) people from thenormal population consisted control group 2.Results. The allele frequencies of HLA B8, B50, C6, C7, DR3, DR7, DQ2, and DR3 homozygosity were higher inthe patient group. HLA DQ2 positivity was 89% in the patient group, 73.9 and 45.5% in control groups 1 and 2,respectively (p <0.0001). HLA A30, C14, DR11, DQ3 frequency were lower in patients compared to both controlgroups. HLA-DR15 alleles in patient and control group 1 was significantly lower compared to the generalpopulation (p <0.05). Thirty (41.1%) patients had typical, 43 (58.9%) patients had atypical presentation. Thirteen(17.8%) patients had other autoimmune diseases. There was no association between coexisting autoimmunediseases and the HLA antigens. Fifteen patients (20.5%) had a positive family history for CD; patients withHLA A69, B41 and C12 alleles had a higher positive family history (p <0.05). Intestinal mucosal damage was asfollows: 5 patients (6.8%) had Marsh 2, 25 (34.3%) Marsh 3a, 28 (38.4%) Marsh 3b, 15 (20.5%) Marsh 3c. Patientswith HLA-DR15 alleles had more frequent Marsh 3a lesions (p <0.05).Conclusions. B8, B50, C6, C7, DR3, DR7, DR3/DR3, DQ2 alleles were risk factors for CD in the Turkish population.HLA C14, DR11, DR15, and DQ3 alleles were found to have a protective role in the same population.