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Background  Drug resistance contributes to the global malaria burden.  Plasmodium   falciparum  dihydrofolate reductase ( dhfr ) and dihydropteroate synthase ( dhps ) polymorphisms confer resistance to sulphadoxine-pyrimethamine (SP).    Methods  The study assessed the frequency of SP resistance-conferring polymorphisms in  Plasmodium   falciparum -positive samples from two clinical studies in Lambaréné. Their role on treatment responses and transmission potential was studied in an efficacy open-label clinical trial with a 28-day follow-up in 29 children under five with uncomplicated malaria.    Results  SP was well tolerated by all subjects in vivo. Three subjects were excluded from per-protocol analysis. PCR-corrected, 12/26 (46%) achieved an adequate clinical and parasitological response, 13/26 (50%) were late parasitological failures, while 1/26 (4%) had an early treatment failure, resulting in early trial discontinuation. Of 106 isolates, 98 (92%) carried the triple mutant  dhfr  haplotype. Three point mutations were found in  dhps  in a variety of haplotypic configurations. The 437G + 540E double mutant allele was found for the first time in Gabon.    Conclusions  There is a high prevalence of  dhfr  triple mutant with some  dhps  point mutations in Gabon, in line with treatment failures observed, and molecular markers of SP resistance should be closely monitored.    Trial Registration  ClinicalTrials.gov:  NCT00453856

High prevalence of dhfr triple mutant and correlation with high rates of sulphadoxine-pyrimethamine treatment failures in vivo in Gabonese children