Consumption of dietary supplements and specifically niche products such as supplements targeting pregnant women is increasing. The advantages of dietary supplementation during pregnancy with folic acid have been established, but health effects of many other supplements have not been confirmed. EU and US legislation on dietary supplements requires the product to be safe for the direct consumer, the mother. Long-term health effects for the fetus due to fetal programming (in utero adaptation of the fetal epigenome due to environmental stimuli such as supplementation) are not taken into account. Such epigenetic alterations can, however, influence the response to health challenges in adulthood. We therefore call for both conducting research in birth cohorts and animal studies to identify potential health effects in progeny of supplement consuming mothers as well as the establishment of a nutrivigilance scheme to identify favorable and adverse effects post-marketing. The acquired knowledge can be used to create more effective legislation on dietary supplement intake during pregnancy for safety of the child. Increasing knowledge on the effects of consuming supplements will create a safer environment for future mothers and their offspring to optimize their health before, during and after pregnancy.