There is increasing evidence, in humans and other mammals, that periconceptional nutritional status influences health in adulthood. This is called ‘foetal programming’ and is likely to be mediated through DNA methylation. Micronutrients, especially B vitamins such as folic acid and vitamin B12 play crucial roles in providing methyl groups for such reactions. This is called epigenetic regulation and may provide some clues to the epidemic of type 2 diabetes and cardiovascular disease. Evidence from mandatory folic acid fortification studies suggests that in the presence of adequate folic acid, neural tube defects due to B12 deficiency have tripled. Such ‘imbalance of high folic acid and low vitamin B12’ in the elderly causes cognitive impairment. A longitudinal study of young women in India showed that children born to those with ‘high folic acid and low B12’ had higher adiposity and insulin resistance. In addition to increased levels of folic acid, B12 deficiency is increasing in countries with mandatory folic acid fortification. Studies on the prevalence of vitamin B12 deficiency during pregnancy and in women of childbearing age, plus the effects of B12 supplementation are therefore urgently needed. This article reviews the role of vitamin B12 during pregnancy on the offspring’s metabolic risk.