Patients living in endemic areas can carry a mixture of Plasmodium falciparum genotypes. To investigate the genetic composition of parasite genotypes in malaria patients during the acute phase of the infection, we performed close follow-ups of 17 Gabonese pediatric patients aged 2-7 years. Capillary blood samples were taken on admission and every 4-6 h after the start of quinine therapy. Merozoite surface protein 2 (MSP2) genotypes were used to assess the parasites' genetic characteristics in each sample. We found that each patient carried parasites with the same genotypic pattern throughout the infection.