Introduction This study aimed to assess the prevalence and associated risk factors of intestinal parasite infections among children less than two years of age in Rutsiro, Rwanda. Methods A cross-sectional parasitological survey was conducted in Rutsiro in June 2016. Fresh stool samples were collected from 353 children and examined using microscopy to detect parasite. A questionnaire was administered to collect data on hygiene, sanitation, socio-demographic and economic characteristics. Results Approximately one in two children (44.8%) were found to be infected with at least one intestinal parasite. Ascaris (28.5%) was the most prevalent infection followed by Entamoeba histolytica (25.95%) and Giardia lamblia (19.6%). Infection with more than one pathogen was noted e.g. presence of Ascaris and yeasts (8.9%), and amoeba with Trichocephale (4.4%), respectively. Children from non-farming families were less likely to be at risk of intestinal parasite infections (AOR = 0.41, p = 0.028) compared to children from farming families. Children from households with access to treated drinking water were less likely to contract intestinal parasite infections (AOR = 0.44, p = 0.021) compared with those who used untreated water. Children from families with improved sources of water were twice as likely to be diagnosed with intestinal parasitoses compared to those who did not. We postulate that the majority of families (50.1%) who have access to improved water sources do not treat water before consumption. Conclusion The high prevalence of intestinal parasitoses in children warrants strict control measures for improved sanitation, while treatment of drinking water should be considered.
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