Background. Ethiopia has one of the highest child malnutrition rates in the world. Food insecurity is one of the determinant factors of malnutrition in developing countries; however its role remains unclear. Objective. To assess household food insecurity and its association with the nutritional status of children 6-59 months of age in East Badawacho District, South Ethiopia. Methods. A community based cross-sectional study was conducted from February 20 to 30, 2014 on a sample of 508 mother/child pairs of 6-59-month-old children. Sample households with eligible children were selected using systematic random sampling technique. Both bivariate and multivariate analysis were used to identify factors associated with nutritional status of children. P value of <0.05 was considered as statistically significant. Result. The prevalence of household food insecurity was 75.8%. The prevalence rates of stunting, underweight, and wasting among children were 45.6%, 26.3%, and 14.6%, respectively. Household food insecurity was significantly associated with underweight (AOR = 3.82; CI = 1.78-8.19) and stunting (AOR = 6.7; CI = 3.71-12.1) but not with wasting. Conclusion and Recommendation. Household food insecurity and the prevalence rates of stunting, underweight, and wasting, among children 6 to 59 months, were high. Intervention programs should focus on improving household food insecurity and nutritional status of children.