To explore the genetic susceptibility of children to vitamin D deficiency rickets through studying the association between Vitamin D receptor (VDR) gene polymorphism and vitamin D deficiency rickets. One hundred and fifty-nine children (100 boys and 59 girls, aged 0 to 2 years), with new-onset vitamin D deficiency rickets were enrolled. The patients sampled from a community of Jiamusi City, Heilongjiang Province. Seventy-eight healthy age-matched children (46 boys and 32 girls) were used as the controls. VDR gene polymorphism (cleaved by restriction endonuclease Fok I) was analyzed by polymerase chase reaction-restriction fragment length polymorphism (PCR-RFLP). The frequencies of the VDR genotype and allele were compared between the two groups. The frequencies of FF, Ff and ff genotypes were 37%, 51% and 12% in the Rickets group, and 18%, 55% and 27% in the Control group. A significant difference was found in the frequency distribution of the VDR genotype between the two groups (chi(2)(0.01(2))=9.210, chi(2)=13.3880, P < 0.01). In the Rickets group, f allele frequency was lower (37% vs 54%), while the F allele was more common than the Control group (63% vs 46%). There is an association between the VDR gene Fok I polymorphism and vitamin D deficiency rickets. The individuals with the F allele are more susceptible to vitamin D deficiency rickets.