Background: Enhanced malaria control has resulted in its reduction in some areas of Sub Saharan Africa including Rwanda. However, asymptomatic hosts serve as a reservoir for the malaria parasite for communities. The objective of this study was to determine the prevalence of malaria parasites and risk factors associated with malaria infection among children underfive years in Huye district, Rwanda.Methods: This community-based cross sectional study was conducted from May to June 2016 among underfive years children. Asymptomatic children underfive years of age were randomly selected from 13 villages. Thick and thin blood smears were prepared from each child for malaria parasite diagnosis. Interviews with parents or guardians were conducted to collect data on malaria associated risk factors. Observations were made of the presence of mosquito breeding sites near and around the homestead.Results: A total of 222 children were included in the study. Nearly a third (28.8%) of the children were within the age of 25-36 months. The majority (54%) of the children were females. Most of the parents/guardians were married (95.9%), nearly all (99.5%) had attended primary school and most (97.3%) were peasants. The overall Plasmodium falciparum prevalence in children was 12.2%. Children aged 1 to 12 months were 3.5 times more likely to have malaria parasites than children aged 13 to 59 months [AOR=3.56; 95%CI=1.18-10.71; p=0.024]. Children who were not sleeping under insecticide treated nets were 15 times more likely to be infected with malaria parasites compared to those who were sleeping under nets [AOR=15.27; 95%CI=4.42-52.82; p<0.001].Conclusion: Malaria parasite prevalence in under-five year children in Huye District, Rwanda is moderate. The asymptomatic infections in the community forms a reservoir for transmission in the area. Young age of the child and not sleeping under mosquito net were associated with malaria parasite infection. The continuing use of mosquito nets needs to be emphasized
