The complexity of Plasmodium falciparum populations in 21 children was studied in repetitive samples over 4 years in an area of Tanzania where the organism is holoendemic. Genotyping was done by a polymerase chain reaction method that targets three highly polymorphic regions of the merozoite surface protein (MSP) 1 block 2, MSP 2, and the glutamine-rich protein. Eight children were repeatedly parasitemic, 5 had scanty parasitemias, and 8 were consistently nonparasitemic. Varying numbers of genotypes were detected in the parasitemic children, but the multiplicity of infection was significantly constant within each child. The children with frequent parasitemias experienced fewer clinical episodes during the study period than those without parasitemias. There was also a tendency for children with more complex infections to experience fewer episodes. The children had consistent parasitologic profiles over the 4 years. Although few subjects were studied and the results will require confirmation, the results suggest that asymptomatic (especially polyclonal) P. falciparum infection protects against clinical disease from new infections.