Several micronutrient deficiencies affect functional, particularly cognition and physical performance of children. Identifying and preventing sub-clinical deficiencies may be important so that adverse effects on functional performance by these deficiencies, particularly of iron and the B vitamins, are prevented. There is also the potential for childhood micronutrient deficiencies to have long-term effects that affect health and productivity in adulthood. This is especially relevant in a developing country such as India, which faces the dual burden of malnutrition and where the prevalence of these deficiencies is high. This review highlights the extent of micronutrient deficiencies in Indian children and focuses on the effect of deficiencies of the B vitamins and iron on cognitive and physical performance in children. Most studies on multiple micronutrient supplementation or fortification in Indian school children show modest effects on cognitive and physical performance, and it is relevant to point out that these studies have largely been conducted on urban children with mild deficiency at most; children with moderate or severe deficiency have not been studied. However, diets of rural children indicate large deficits in micronutrient intake, particularly of folic acid, riboflavin and iron, and their consequences have not been studied. With the limited evidence available, a short term but economical solution to ensure adequate micronutrient intakes could be through the fortification of staple cereals taken throughout the day. As increasing household incomes translate into an increase in food expenditure and diet diversification, it may become necessary to define upper limits of intake for nutrients in India, particularly as many commercial foods are fortified.