Background: Malnutrition is a major public health concern affecting a significant number of school children influencing their health, growth and development, and school academic performance.Objective: To determine the nutritional status of school children in terms of stunting, underweight and thinness and to identify its correlates at Fogera woreda, Northwest Ethiopia, 2012.Methods: Institutional and community based cross sectional study was conducted from June to December, 2012. The study included 790 primary school children who were selected from the source population by multi stage random sampling technique. Data were collected through interview with parents with a standardized and pretested questionnaire; microscope, physical examination and anthropometric measuring and data were entered and analyzed using SPSS version 16.0 and AnthroPlus softwares. Binary and Multivariate logistic regression analyses were used to identify factors associated with malnutrition among school children.Results: Prevalence of malnutrition was high among school children aged six to fourteen years old (mean age 11.4 ± 2.1 years); Study contents include questionnaire surveys, anthropometric measurement, observation and laboratory methods. Finally 790 school-age students took part in study. The results showed that the overall prevalence of stunting, underweight and thinness were 243 (30.7%), 96 (59.7%) and 294 (37.2%). Those children who were found to be both stunted and underweight were only 1.01% (8). Rice consumption, family size, Family radio, infection, vaccination, latrine availability were significantly associated with malnutrition. However, statistically significant association was not found between malnutrition and parasitic infection and other health conditions. Conclusion:In concluding, the study found high prevalence of malnutrition (stunting, thinness and underweight). Vaccination, family planning, latrine construction and utilization, rice production and prevention and early treatment of infection were identified as essential interventions to reduce the risk of malnutrition. Ownership of radio should be promoted to reduce malnutrition. However, parasitic infection among primary school children was not significantly associated with malnutrition. But, school children should be targeted to deworming to treat parasitic infections.