A mutation-specific polymerase chain reaction method was used to estimate the proportion of pyrimethamine-resistant parasites in 101 children reporting with malaria at the hospital in Ifakara, a town in southern Tanzania. The method is based on the observation that a point mutation (Asn-108) in the dihydroifolate reductase gene confers resistance to pyrimethamine. Twenty-eight percent of the examined 101 children had pyrimethamine-resistant parasites, 65% had pyrimethamine-sensitive parasites with the wild-type Ser-108 codon, and 9% had both alleles, suggesting a mixed infection. None of the 21 children with clinical malaria had pyrimethamine-resistant parasites. Currently, sulfadoxine-pyrimethamine is considered a potential first-line drug for malaria treatment in most African countries. We suggest that although sulfadoxine-pyrimethamine could still be effective against chloroquine-resistant malaria in this area, its judicious use is important so as to minimize the spread of resistance.