Folic acid and iron supplementation has historically been recommended as the preferred anaemia control strategy among preschoolers in sub-Saharan Africa and other resource-poor settings, but home fortification of complementary foods with multiple micronutrient powders (MNPs) can now be considered the preferred approach. The World Health Organization endorses home fortification with MNPs containing at least iron, vitamin A and zinc to control childhood anaemia, and calls for concomitant malaria control strategies in malaria endemic regions. Among other micronutrients, current MNP formulations generally include 88 μg folic acid (corresponding to 100% of the Recommended Nutrient Intake). The risks and benefits of providing supplemental folic acid at these levels are unclear. The limited data available indicate that folate deficiency may not be a major public health problem among children living in sub-Saharan Africa and supplemental folic acid may therefore not have any benefits. Furthermore, supraphysiological, and possibly even physiological, folic acid dosages may favour Plasmodium falciparum growth, inhibit parasite clearance of sulphadoxine-pyrimethamine (SP)-treated malaria and increase subsequent recrudescence. Even though programmatic options to limit prophylactic SP use or to promote the use of insecticide treated bed nets may render the use of folic acid safer, programmatic barriers to these approaches are likely to persist. Research is needed to characterise the prevalence of folate deficiency among young children worldwide and to design safe MNP and other types of fortification approaches in sub-Sahara Africa. In parallel, updated global guidance is needed for MNP programmes in these regions.