BACKGROUND The cause of under-nutrition in schoolchildren is complex and varying from region to region. However, identifying the cause is the basic step for nutritional intervention programs. METHODS School based cross-sectional survey was conducted among 450 schoolchildren aged 7-14 years, using multi-stage sampling techniques in Dale Woreda, southern Ethiopia. A structured questionnaire and 24-hour recall methods were administered to determine the sociodemographic and dietary intake of participants. Stool microscopic examination was done. Weight and height were measured using a standard calibrated scale. Odds ratio generated from logistic regression was used to determine the strength of variables association. RESULTS Older age group (10-14 vs. 7-9) (AOR = 3.4; 95% CI, 1.7-6.6) and having Trichuris Trichura infection (AOR = 3.9; 95% CI, 1.4 -11.6) increased the risk of being stunted. Children whose mothers have completed primary education are less likely to be stunted than children whose mothers do not have formal education (AOR = 0.3; 95% CI, 0.2-0.8). Having large family size (AOR = 3.3; 95% CI, 1.4-7.9) and inadequate intake of carbohydrate (AOR = 3.1; 95% CI, 1.4-6.8) were independent predictors of wasting. Children whose mothers completed primary education are less likely to be underweight (AOR = 0.3; 95% CI, 0.1-0.9). Children live in food insecure households are more likely to be stunted, under-weight and wasted than children live in food secure households (AOR = 2.5; 95%, 1-5.6; AOR = 3.9; 95% CI, 1.2-12.0; AOR = 4.8; 95% CI, 1.7-13.6;). CONCLUSIONS Household food insecurity, low maternal education and infection with Trichuris trichura were some of the major factors contributing to under-nutrition in the study area.