The development of resistance to sulfadoxine-pyrimethamine by Plasmodium parasites is a major problem for the effective treatment of malaria, especially P. falciparum malaria. Although the molecular basis for parasite resistance is known, the factors promoting the development and transmission of these resistant parasites are less clear. This paper reports the results of a quantitative comparison of factors previously hypothesized as important for the development of drug resistance, drug dosage, time of treatment, and drug elimination half-life, with an in-host dynamics model of P. falciparum malaria in a malaria-naïve host. The results indicate that the development of drug resistance can be categorized into three stages. The first is the selection of existing parasites with genetic mutations in the dihydrofolate reductase or dihydropteroate synthetase gene. This selection is driven by the long half-life of the sulfadoxine-pyrimethamine combination. The second stage involves the selection of parasites with allelic types of higher resistance within the host during an infection. The timing of treatment relative to initiation of a specific anti-P. falciparum EMP1 immune response is an important factor during this stage, as is the treatment dosage. During the third stage, clinical treatment failure becomes prevalent as the parasites develop sufficient resistance mutations to survive therapeutic doses of the drug combination. Therefore, the model output reaffirms the importance of correct treatment of confirmed malaria cases in slowing the development of parasite resistance to sulfadoxine-pyrimethamine.Drug resistance is becoming an increasingly important factor in the effective treatment of malaria. High levels of resistance to chloroquine have forced some countries to switch their first-line drug to sulfadoxine-pyrimethamine (SP, trade name Fansidar). However, resistance to this drug combination is developing fast, with treatment failure being reported in Africa, Asia, Indonesia, and South America (5,7,16,20,31).Pyrimethamine and sulfadoxine act synergistically to inhibit two enzymes important in the parasite's folate biosynthetic pathway, dihydrofolate reductase (DHFR) and dihydropteroate synthetase (DHPS) (13). Point mutations in the DHFR and DHPS genes confer resistance to pyrimethamine and sulfadoxine, respectively, with decreasing in vitro Plasmodium falciparum susceptibility related to the number of mutations in each gene (6,30,34). The same mutations have been linked to treatment failure in the clinical setting (5,7,20,33); the presence of mutations in DHFR appear to be more important in causing treatment failure than DHPS mutations (5). Although the molecular basis for SP resistance is understood, the factors promoting the development and transmission of these mutants are less clear.It has been suggested that drug pharmacokinetics (12), overusage of drugs (28), cross-resistance between drugs (14), and inadequate treatment through inappropriate prescription or administration, noncompliance, or poor absorption...