Urbanization may increase the risk of human infection with intestinal helminths. A cross-sectional survey was conducted to investigate the prevalence, intensity and potential risk factors of acquiring such infection, among children aged 3-14 years in similar urban and rural communities in southern Malawi. Stool samples were collected from 553 children (273 urban and 280 rural). The overall prevalence of helminth infection was significantly higher in the urban subjects than in the rural (16.5% v. 3.6%; P < 0.001), mostly because of differences in the prevalence of Ascaris lumbricoides infection. Living in an urban community was associated with a significantly higher risk of infection [odds ratio (OR) = 5.3; 95% confidence interval (CI) = 2.6-12.1], even after controlling for potential confounding factors. In the urban community, risk factors included having pools of water/sewage around houses (OR = 3.0; CI = 1.4-6.5), not wearing shoes (OR = 7.1; CI = 2.7-19.2), not attending school (OR = 2.8; CI = 1.2-6.5), having mothers with 4-8 years of education (OR = 5.2; CI = 2.0-14.0), and having mothers below 35 years of age (OR = 4.09; CI = 1.39-16.28). In this part of Africa, efforts to reduce helminth infections may best be focused on reducing geohelminth burden in urban areas.