Previous studies have shown a high rate of neural tube defects (NTD) in Gorgan, northern Islamic Republic of Iran. This case–control study during 2003–04 compared serum zinc levels and other variables in 23 mothers of neonates affected with NTD and 36 mothers with normal healthy neonates in Dezyani hospital in Gorgan. Mean serum zinc levels in the case and control groups were 13.43 µmol/L (SD 6.3) and 11.41 µmol/L (SD 6.3) respectively. Zinc deficiency was found in 13 (36.5%) of the cases and 7 (19.4%) of the controls. Logistic regression analysis showed an association between the presence of NTD and zinc deficiency (OR 5.06; 95% CI 1.51–16.94).