Maternal vitamin D deficiency is considered to be the key determinant of the development of neonatal vitamin D deficiency at birth and during early infancy. Specific vitamin D receptor (VDR) gene polymorphisms have been associated with adverse pregnancy and offspring outcomes. The aim of this study was to evaluate the effect of maternal and neonatal VDR polymorphisms (ApaI, TaqI, BsmI, FokI, Tru9I) on maternal and neonatal vitamin D status. VDR polymorphisms were genotyped in 70 mother-neonate pairs of Greek origin, and classified according to international thresholds for Vitamin D status. Mean neonatal and maternal 25-hydroxy-vitamin D [25(OH)D] concentrations were 35 ± 20 and 47 ± 26 nmol/l, respectively. Neonatal VDR polymorphisms were not associated with neonatal 25(OH)D concentrations. In contrast, mothers with the Fokl FF polymorphism had a 70 % lower risk of vitamin D deficiency [25(OH)D <30 nmol/l] compared with ff ones, after adjustment for several confounders. They were also in 73 % and 88 % lower risk of giving birth to vitamin D deficient [25(OH)D <30 nmol/l] neonates compared with Ff and ff mothers, respectively. These results suggest a protective role of maternal Fokl FF genotype against both maternal and neonatal vitamin D deficiency. Further studies are needed to clarify the complex gene-gene and gene-environment interactions that determine vitamin D status at birth.