Iron and zinc deficiencies are common in developing countries and supplementation is one way of reversing these deficiencies. The objective of this randomized, placebo-controlled clinical trial was to identify the effect of daily supplementation with iron, zinc, and iron plus zinc on the morbidity experience of 855 children 0.5-15 years of age in Peru. Single nutrient supplementation with zinc reduced diarrhea morbidity by 23% in all children. In older children (more than five years of age), iron supplementation increased morbidity due to Plasmodium vivax and diarrhea. In younger children, iron combined with zinc provided protection against P. vivax malaria, but also interfered with some of the diarrhea protection associated with zinc supplementation. No statistically significant effect was observed of either supplement on incidence of respiratory infection or anthropometric indices. Iron and zinc deficiencies should be remedied, and combined supplementation may be a good option, particularly in younger children in P. vivax malaria-endemic areas, although local endemicity and species-specific prevalence should be considered carefully when designing any supplementation program involving iron in a malaria-endemic area.