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<p>Abstract</p> <p>Background</p> <p>Long-lasting insecticidal nets (LLINs) are an important tool for controlling malaria. Much attention has been devoted to determine both the effect of LLINs on the reduction of <it>Plasmodium </it>infection rate and on clinically-confirmed malaria cases in sub-Saharan Africa. We carried out an epidemiological study to investigate whether LLINs impact on <it>Plasmodium </it>prevalence rate and the proportion of clinically-confirmed malaria cases, in five villages in the district of Toumodi, central Côte d'Ivoire.</p> <p>Methods</p> <p>From April 2007 to November 2008, a community-based malaria control programme was implemented in the study villages, which involved large-scale distribution of LLINs, and training and sensitization activities within the community. We determined the effect of this programme on <it>Plasmodium </it>prevalence rate, clinically-confirmed malaria cases and proportion of high parasitaemia rates in children aged 6-59 months through a series of cross-sectional surveys starting in April 2007 and repeated once every 6 months.</p> <p>Results</p> <p>We observed a significant decrease in the mean <it>P. falciparum </it>prevalence rate from April 2007 to April 2008 (p = 0.029). An opposite trend was observed from November 2007 to November 2008 when <it>P. falciparum </it>prevalence rate increased significantly (p = 0.003). Highly significant decreases in the proportions of clinical malaria cases were observed between April 2007 and April 2008 (p < 0.001), and between November 2007 and November 2008 (p = 0.001).</p> <p>Conclusions</p> <p>Large-scale distribution of LLINs, accompanied by training and sensitization activities, significantly reduced <it>Plasmodium </it>prevalence rates among young children in the first year of the project, whereas overall clinical malaria rates dropped over the entire 18-month project period. A decrease in community motivation to sleep under bed nets, perhaps along with changing patterns of malaria transmission, might explain the observed increase in the <it>Plasmodium </it>prevalence rate between November 2007 and November 2008.</p>