In the absence of a firmly established gene responsible for chloroquine and amodiaquine resistance in Plasmodium falciparum, surveillance of resistance to these first-line drugs in Cameroon needs to be performed by in vivo or in vitro tests for drug resistance. These 2 methodological approaches to define drug resistance were shown to be complementary and concordant in a majority of cases at our study sites, but discordant results may be observed in a few cases, probably as a result of acquired immunity and low plasma drug levels. To further examine the nature of recrudescent and persistent parasitemia after treatment with chloroquine or amodiaquine, the clinical response of children aged < 5 years, presumably with insufficient immune response, was assessed, and the in vitro response of the corresponding isolates was determined if treatment or parasitological failure occurred. Genotyping of pretreatment and posttreatment isolates was performed by polymerase chain reaction to distinguish between recrudescence and reinfection. Plasma drug levels were measured at the time of therapeutic failure by high-performance liquid chromatography. All cases of therapeutic or parasitological failure observed on or before Day 14 were due to the persistence or recrudescence of the original parasite populations present before treatment, with or without selection and appearance of new populations. Most parasites were characterized by elevated 50% inhibitory concentrations for chloroquine and amodiaquine at the time of clinical or parasitological failure. In some children, recrudescence was explained by the absence of drug in the plasma. The simultaneous analysis of clinical and in vitro responses, plasma drug level measurement, and genotyping may yield results that may explain the reasons for therapeutic failure, help establish the threshold level for in vitro resistance, and provide a set of more accurate tools to describe the epidemiology of drug-resistant P. falciparum while awaiting for the identification of the chloroquine and amodiaquine resistance gene or genes.