The effects of drugs on Plasmodium falciparum transmission stages may reduce the spread of parasites in the population and contribute to malaria control. Detailed quantitative studies on (sub)microscopic gametocytaemia have become feasible with the availability of real-time Pfs25 quantitative Nucleic Acid Sequence-based Amplification (QT-NASBA), which can be used to detect gametocyte densities above 20 gametocytes per millilitre from in vitro cultures. Gametocyte dynamics were investigated in children with uncomplicated P. falciparum malaria after treatment with sulphadoxine-pyrimethamine (SP) or a combination of SP and artesunate (SP+AS), in a 28-days drug efficacy study. This study demonstrated that gametocyte prevalence in 873 samples from symptomatic Kenyan children was 2.8 times higher by QT-NASBA compared with microscopy. Microscopy-positive cases showed a significant correlation with QT-NASBA for gametocyte density. At enrolment, gametocyte prevalence was 86% by QT-NASBA compared with 22% by microscopy. Gametocytes were detected in 97% of children in at least one blood sample and in 38% of children in all samples obtained during the 28-days follow-up. Both the risk of gametocyte carriage and gametocyte density were considerably higher after treatment with SP compared with SP+AS. Gametocyte prevalence and density decreased with time in the SP+AS group, but not in the SP-treated children. Our data suggest that the potential of malaria transmission remains high even after treatment with artemisinin combination therapy, although prevalence and density of gametocytes is lower after SP+AS.