The World Health Organization recommends deworming of children aged 12-24 months in highly endemic areas. Our research objectives were to: 1) examine prevalence patterns of helminth infection in early childhood; 2) assess the association between helminth infection and socio-demographic characteristics; and 3) examine the effect of the intensity of helminth infection on stunting and anemia. A survey of children (7-9 and 12-14 months) living in Belén (Peru) was undertaken between July 2007 and February 2008. A questionnaire was administered to obtain socio-demographic characteristics, blood and stool samples were collected, and length-for-age Z scores were calculated. The Kato-Katz method was used to determine the prevalence and intensity of Ascaris, Trichuris, and hookworm infections. Of 370 participating children, 349 had parasitological results. Infections first appeared in children at 8 months of age. The prevalence of any helminth infection increased linearly to approximately 37.0% (95%CI: 24.3-51.3%) by 14 months of age. Multivariate analysis showed that age, female sex, and residing in the floodplain were significant determinants of helminth infection. Among infected children, moderate-to-heavy infection of any helminth was associated with stunting (βadjusted=-0.84; 95%CI: -1.48, -0.20). These results support the implementation of deworming programs aimed at young children in highly endemic areas. © 2010 Royal Society of Tropical Medicine and Hygiene.