VDR and vitamin D deficiency: This study showed a consistent pattern effect of vitamin D deficiency and SNPs on birth anthropometry: (1) maternal vitamin D deficiency (25OHD <30 nmol/L) demonstrated consistent associations on birth weight, head circumference and crown–heel length at birth in all the analyses; (2) neonatal SNPs, VDR rs2228570 and GC rs4588, demonstrated significant associations with birth weight and head circumference, respectively; and (3) a potential interaction was observed between maternal VDR rs2228570 with maternal vitamin D deficiency on head circumference.