Vitamin D deficient rickets is prevalent in Turkey and a considerable number of children are at risk of growth retardation, impaired bone formation and fracture. In order to check whether vitamin D receptor (VDR) gene polymorphism relates to the vitamin D deficient rickets, we analyzed VDR gene FokI, TaqI and ApaI polymorphisms in 24 Turkish vitamin D deficient rickets patients and 100 healthy controls. We found that "A" (ApaI) allele is more abundant in patients than controls (83 vs 57%, p = 0.002) but there were no significant differences for FokI (p = 0.693) and TaqI (p = 0.804) allele frequencies between patients and controls. We also showed that the frequency of Tt and Aa genotypes was significantly decreased in patients. Our results indicated that VDR gene polymorphisms might be an important factor for genetic susceptibility to vitamin D deficient rickets in the Turkish population.