To explore whether maternal vitamin B12 and folate status during early pregnancy are associated with cardiometabolic risk factors in the offspring at age 5–6. Prospective multi-ethnic birth cohort, the Amsterdam Born Children and their Development study (ABCD). 12 373 pregnant women living in Amsterdam were approached between 2003 and 2004 for participation in the study. Mother–child pairs for whom information on maternal vitamin B12 or folate status in early gestation and health at age 5–6 years was available (n = 1950). Vitamin B12 and folate concentrations were determined in maternal serum at intake in early pregnancy (median 13 weeks' gestation). Anthropometric measurements, blood pressure and fasting blood samples were collected during a health check of children aged 5–6 years. Multiple linear regression was performed to investigate the association between maternal serum concentrations and children's outcomes, corrected for confounders. Gestational age at birth, birthweight, body mass index (BMI), glucose levels, triglyceride levels, blood pressure and heart rate of the offspring at age 5–6. Low maternal folate levels during early pregnancy were associated with slightly higher BMI in the offspring [decrease per 10 units: β 0.07 kg/m2, 95% confidence interval (CI) 0.01, 0.13]. Low maternal vitamin B12 concentrations were associated with higher heart rates (decrease per 100 units: β 0.49 beats/min, 95% CI 0.11, 0.87). This study provides further evidence that maternal nutrition in early pregnancy may possibly program cardiometabolic health of the offspring. Low folate and vitamin B12 levels during pregnancy are associated with higher BMI and heart rate in offspring.