Objectives: Childhood malnutrition is a major concern in developing countries. Therefore, the present study aimed to determine the nutritional status and dietary habits of school children. Methods: This is a community based cross-sectional survey designed to evaluate nutritional status of students aged (5 -19 years) in Beni-Suef Governorate, Egypt, during September-December 2013. A two-stage sampling technique was done; 22 government schools were selected in the first stage. In the second stage, 1100 students were selected from the target population of the study. Weight, height, and age data were used to calculate z-scores of the three different nutritional indicators. Dietary habits were studied using a food frequency questionnaire. Results: Underweight (WAZ < −2) and stunting (HAZ < −2) occurred in 10% and 53.2%, respectively. WAZ and HAZ mean scores of the children were −0.22 (SD = 1.39) and −2.09 (SD = 2.03), respectively. The malnourished children were classified on the basis of (WHO/NCHS) reference population BMI z-scores as being: 2.8% underweight (<−2SD) and 34.4% obese (>+2SD). Boys were more underweight (3%) than girls (2.2%). Conversely, girls tend to be more stunted (65.3%) compared to boys (59.9%) in the age group 10 -14 years. Identified risk factors associated with malnutrition for those aged more than 10 years were: mother education (P-value = 0.03), father education (P-value = 0.04) and family size (P-value = 0.014). Conclusıon and Recommendatıons: Child's nutritional status is strongly associated with the literacy of both parents and family size. The prevalence of malnutrition can be reduced by implementation of school intervention programs for the socioeconomic development.