The prevalence of soil-transmitted helminthiasis is close to half the population in Central America, with the marginalized peri-urban poor disproportionately affected. Previous single province helminth surveys conducted in Nicaragua have shown Ascaris lumbricoides to be the predominant species. In 2005, we conducted a cross-sectional study of 880 children in 10 Nicaraguan primary schools located in four provinces. We aimed to establish the prevalence and intensity of soil-transmitted helminth infections and to investigate the factors associated with helminthiasis. Almost half (46%) of the children were infected with soil-transmitted helminths. Tichuris trichiura was the most common infective species (34.7%). The prevalence and intensity of helminthiasis was heterogeneous in the provinces, with children educated in peri-urban schools most affected. Healthy policies are required that favour the peri-urban poor who have inadequate and declining access to water and sanitation.