Sulphadoxine/pyrimethamine (SP) has become the first-line treatment of uncomplicated malaria in a number of African countries. Molecular surveillance of resistance-mediating mutations in Plasmodium falciparum dihydrofolate reductase (dhfr) and dihydropteroate synthase (dhps) has been proposed as a means of predicting SP treatment outcomes, but optimal methods of surveillance in different populations have not been well established. To investigate the relationship between molecular markers of SP resistance, host immunity, and response to therapy, we evaluated the association between the presence of five key dhfr and dhps mutations at enrollment and clinical outcome in children and adults treated with SP for uncomplicated malaria in Kampala, Uganda. Clinical treatment failure was 11% at 14 days, increasing to 30% at 28 days, after excluding new infections. Outcomes varied markedly based on the number of dhfr and dhps mutations and on the age of treated subjects. All infections with less than two dhfr/dhps mutations were successfully treated. Treatment failure associated with any two, three, or four dhfr/dhps mutations occurred in nine of 24 (38%) children up to 5 years, but not in older patients (0/20). In the presence of all five mutations, treatment failure occurred equally in children aged 5 years or younger [7/16 (44%)] and in older patients [8/16 (50%)]. Our results showed that age, a surrogate marker of antimalarial immunity, had a major impact on the relationship between polymorphisms in SP target enzymes and treatment outcomes. The use of molecular markers of SP resistance to predict treatment failure rates should take age into account.