Giardia duodenalis infection is highly prevalent and a cause of underweight in pre-school children in rural Rwanda. The present study aimed at assessing the age-pattern of Giardia infection and its manifestation in older children, i.e., during school age. Stool samples were collected from 622 schoolchildren at two schools in the Huye district of southern Rwanda (rural, 301; urban, 321) and subjected to G. duodenalis specific PCR assays. Clinical and anthropometric data, socio-economic status and factors potentially associated with G. duodenalis infection were assessed. Of the 622 children (mean age, 10.4 years), 35.7% were infected with G. duodenalis (rural, 43.9%; urban, 28.0%; P<0.0001). Only few indicators of low socio-economic status were found to be associated with infection. In rural but not urban schoolchildren, infection prevalence declined significantly with age. G. duodenalis infection more than doubled the odds of stunting in both rural (adjusted OR, 2.35 (95%CI, 1.25-4.41)) and urban children (adjusted OR, 2.27 (95%CI, 1.01-5.09)). In the study area of rural southern Rwanda, G. duodenalis prevalence among children declined throughout school-age. The data suggest that while lacking overt clinical manifestation at high endemicity, G. duodenalis infection is a common cause of stunting in schoolchildren.