Malnutrition in school-age children is common in developing countries and includes both stunting and underweight. Stunting, which represents a chronic state of nutritional stress, leads to adverse health, educational and cognitive effects. Although much research is focused on preschool-age children, recent studies show both the high prevalence of stunting and the effectiveness of interventions in school-age children. The objectives of the current study were to determine the risk factors for stunting only, and stunting and underweight. A survey was conducted in 1074 grade 5 children (mean age 10 years) from 17 schools in Belen, Peru, a community of extreme poverty. Prevalence of underweight and stunting were 10.5 and 34.5%, respectively, co-prevalence was 9.3%. Based on multivariable logistic regression analyses, significant independent risk factors (odds ratio: OR) for stunting and underweight were: age (per 1 year increment) (OR=1.55; 95% confidence interval (CI): 1.33, 1.81); diarrhoea in the last week (OR=1.96; 95% CI: 1.17, 3.29) and hookworm infection (OR=1.74; 95% CI: 1.05, 2.86). Significant independent risk factors for stunting only were: age (per 1 year increment) (OR=1.51; 95% CI: 1.35, 1.70); anaemia (OR=1.98; 95% CI: 1.26, 3.11); and moderate and heavy Trichuris and Ascaris co-infection (OR=1.95; 95% CI: 1.35, 2.82). Our results indicate a high prevalence of stunting, in addition to other adverse health indicators, in the study population. Due to the interrelation between many of these health and nutrition problems, interventions at both the school and community levels, including de-worming, feeding programs and health and hygiene education, are needed to reduce malnutrition in this and other similar populations living in conditions of extreme poverty.