Hymenolepis nana is the most common cestode infection in the world. However, limited information is available regarding its impact on affected populations. We studied the epidemiology and symptoms associated with hymenolepiasis among children 3-16 years old in 16 rural communities of the highlands of the Cusco region in Peru. Information on demographics, socioeconomic status, symptoms as reported by parents, and parasitological testing was obtained from the database of an ongoing Fasciola hepatica epidemiologic study. A total of 1,230 children were included in the study. Forty-five percent were infected with at least one pathogenic intestinal parasite. Giardia spp. (22.9%) was the most common, followed by Hymenolepis (17.4%), Fasciola (14.1%), Ascaris lumbricoides (6.1%), and Strongyloides stercoralis (2%). The prevalence of Hymenolepis infection varied by community, by other parasitic infections, and by socioeconomic status. However, only years of education of the mother, use of well water, and age less than 10 years were associated with Hymenolepis infection in the multivariate analysis. Hymenolepis nana infection was associated with diarrhea, jaundice, headaches, fever, and fatigue. Children with > 500 eggs/g of stool were more likely to have symptoms of weight loss, jaundice, diarrhea, and fever. Hymenolepis nana infection and age were the only factors retained in the multivariate analysis modeling diarrhea. Hymenolepiasis is a common gastrointestinal helminth in the Cusco region and is associated with significant morbidity in children in rural communities. The impact caused by the emergence of Hymenolepis as a prevalent intestinal parasite deserves closer scrutiny.