Background: Vitamin D (VD) is a remarkable problem during pregnancy. VD plays a crucial role in cellular growth and differentiation during embryogenesis. VD deficiency in pregnancy is associated with various maternal and neonatal comorbidities.  Aim: In this study, we aimed to evaluate the potential association between maternal and neonatal vitamin D status and the subsequent development of congenital anomalies. Patients and methods: A case-control study involving 30 mothers and their neonates born with gross structural congenital anomalies as cases and 30 mothers and their healthy neonates as controls recruited from Ain Shams University Children Hospital. Maternal and Neonatal blood samples were obtained to determine serum 25-hydroxyvitamin D.  The 25-hydroxyvitamin D concentration was stratified into a severe deficient<10ng/ml, deficient <20ng/ml, insufficient 20-29ng/ml and sufficient >30ng/ml. Status above 150ng/ml presents high risk of toxicity.  Results: There were statistically significant differences between the two groups regarding maternal and neonatal vitamin D serum level within 29 days postpartum. Mean maternal vitamin D level in cases was 23.8ng/ml versus 42.13ng/ml in controls (P = 0,000). Mean neonatal vitamin D level in cases was 15.97ng/ml versus 28.9ng/ml in controls (P = 0,000).There was significant positive correlation between both maternal and neonatal vitamin D level with birth weight. Conclusion: A compromised maternal vitamin D status is associated with an increased prevalence of congenital anomalies in offspring. Therefore, improvement of the periconceptional maternal vitamin D status is recommended.