Intermittent preventive treatment for malaria in infants (IPTi) is a promising malaria control strategy. However, mass preventive treatment for malaria inherently bears the risk of increasing drug resistance. Here, the effect of single-dose sulfadoxine-pyrimethamine (S-P) versus placebo on Plasmodium falciparum infection rates was assessed in 63 selected infants who were aparasitemic at enrollment. An increase in the proportion of infants with isolates exhibiting drug resistance-associated mutations was detected 3 weeks after drug application in the treatment group. S-P, in the setting of IPTi, appears to cause a parasitological rebound effect in which there is selection of drug-resistant parasites for a short period after drug clearance.