There is a high prevalence of fascioliasis in the Peruvian highlands, but most cases remain undiagnosed. The burden of disease caused by chronic subclinical infection is largely unknown. We studied school-age children from a district in Paucartambo Province in Cusco, Peru to evaluate the burden of disease caused by subclinical fascioliasis. Parasite eggs and/or larvae were identified in 46.2% of subjects, including Fasciola hepatica in 10.3% of subjects. Fascioliasis was independently associated with anemia (adjusted odds ratio = 3.01 [1.10-8.23]). Subclinical fascioliasis was common among children and strongly associated with anemia. Anemia should be recognized as an important component of the burden of disease from fascioliasis.