Purpose: Polymorphisms in cytokine genes can determine their level of expression and affect the phenotypic expression of immunomediated diseases, such as celiac disease (CD). We thus evaluated cytokine polymorphism prevalence in CD patients and population controls, and assessed the correlation between specific polymorphisms and celiacs' clinical characteristics. Methods: 155 CD patients and 202 population controls were enrolled in the study. Cytokine polymorphisms (TNF␣ Ϫ308 and Ϫ238, IL-1 Ϫ511 and ϩ3954, IL-1b RN ϩ 2018, IL-6 Ϫ174, IL-10 Ϫ1082, Ϫ819 and Ϫ592, TGF1 ϩ 29 and ϩ74, IFN-␥ ϩ 874) and HLA class II alleles were determined by sequence-specific primer polymerase chain reaction or restriction fragment length polymorphism analysis. Duodenal histology was classified using Marsh's criteria. Variables significantly associated with CD patients' characteristics were identified by multivariate logistic regression analysis. Results: A significantly higher frequency of Ϫ308 TNF␣ polymorphism was observed in CD patients compared to the entire population control group, although no difference was detected when population controls were stratified according to HLA class II. Among celiacs, early onset of the disease (Յ2 year old) and the presence of a severe intestinal lesion (Marsh 3C) were significantly associated with the Ϫ1082 A/A IL-10 genotype which corresponds to a low producer phenotype (OR 3.28, respectively). Conclusion: The association between IL-10 genotypes and both histological severity at diagnosis and age of onset could be related to an alteration in cytokine balance, and supports the idea that the various clinical manifestations of the disease could be determined by a different genetic background. Genet Med 2006:8(3):169-174.