Micronutrient deficiencies (MNDs) have severe health consequences and are particularly harmful during early childhood due to their impact on the physical and cognitive development of children.We carry out a health economic study on the burden of MNDs in 6-59 months old children and of interventions promoting pre-fortified packaged foods. The burden of MNDs in the Philippines is assessed by building a model simulating the consequences of MNDs in childhood over the future lifetime of children. Effectiveness of food fortification in controlled trials is examined by performing a systematic review and meta-analysis of fortification trials.Main results: Iron, vitamin A and zinc deficiencies lead to substantial costs in terms of direct medical costs (29 million dollars), production losses (of 462 million dollars) and disability adjusted life years (116,656 DALYs) in 6-59 months old children the Philippines. Costs are highly concentrated in the lower socio-economic strata and in children 6-23 months old. Multi micronutrient fortified milk and cereal products can be an effective option to reduce anemia of children up to three years of age as risk of anemia is reduced by 57% (absolute risk reduction 22%; NNT 5).