The inability to distinguish recrudescent Plasmodium falciparum infections (treatment failures) from reinfections (new infections) is an important impediment to the evaluation of antimalarial treatment regimens. Ten paired primary and recrudescent isolates collected near the Thai-Cambodian border were analyzed by restriction fragment length polymorphism (RFLP) and by polymerase chain reaction (PCR) genotyping of the genes encoding the following proteins: circumsporozite (CS) protein, erythrocyte binding antigen (EBA)-175, ring-infected erythrocyte surface antigen (RESA), merozoite surface protein-1 (MSP-1), and MSP-2. Both methods demonstrated that the fingerprint pattern of each recrudescent isolate was identical to or was contained within the pattern of the primary isolate. Each recrudescent isolate was unique when compared with the other nine primary isolates. Typing by PCR was more sensitive for the detection of multiclone infections and could be performed with small volumes of whole blood. The PCR genotyping could be a practical method for distinguishing a recrudescent from a new infection when treatment studies are conducted in areas with active malaria transmission.