The results of investigation of influence of immune defense modifier genes polymorphism: IL1B (+3953A1/A2), IL1RN (VNTR), IL4A (3'-UTR G/C), IL4RA (I50V), IL12B (1188A/C) and VDR (F/f and B/b) on celiac disease development and various clinical features of disease are presented. The study was performed in 49 families with proband affected by celiac disease (139 people) and 129 unaffected controls of Russian ethnicity from Tomsk. No associations were shown between these alleles and celiac disease by case-control study. However, in family-based investigation, the association was detected for 3'-UTR G/C polymorphism of IL4 gene (p = 0.024). Furthermore, for this polymorphic variant the associations with atypical form of the disease was shown (p = 0.001), as well as with osteopenic (p = 0.039) and thyriopatic (p = 0.042) complications of celiac disease. Association with clinical course of the disease (typical form) was obtained for 150V polymorphism of IL4RA gene and for F/f polymorphism of VDR gene (p = 0.001 and p = 0.009, respectively). Thus, in this investigation it was detected that the associations with the studied phenotypes were found mainly for polymorphic variants of Th2-immunity genes.