BackgroundMore than one-third of deaths during the first five years of life are attributed to undernutrition, which are mostly preventable through economic development and public health measures. To alleviate this problem, it is necessary to determine the nature, magnitude and determinants of undernutrition. However, there is lack of evidence in agro-pastoralist communities like Bule Hora district. Therefore, this study assessed magnitude and factors associated with undernutrition in children who are 6–59 months of age in agro-pastoral community of Bule Hora District, South Ethiopia.MethodsA community based cross-sectional study design was used to assess the magnitude and factors associated with undernutrition in children between 6–59 months. A structured questionnaire was used to collect data from 796 children paired with their mothers. Anthropometric measurements and determinant factors were collected. SPSS version 16.0 statistical software was used for analysis. Bivariate and multivariate logistic regression analyses were conducted to identify factors associated to nutritional status of the children Statistical association was declared significant if p-value was less than 0.05.ResultsAmong study participants, 47.6%, 29.2% and 13.4% of them were stunted, underweight, and wasted respectively. Presence of diarrhea in the past two weeks, male sex, uneducated fathers and > 4 children ever born to a mother were significantly associated with being underweight. Presence of diarrhea in the past two weeks, male sex and pre–lacteal feeding were significantly associated with stunting. Similarly, presence of diarrhea in the past two weeks, age at complementary feed was started and not using family planning methods were associated to wasting.ConclusionUndernutrition is very common in under-five children of Bule Hora district. Factors associated to nutritional status of children in agro-pastoralist are similar to the agrarian community. Diarrheal morbidity was associated with all forms of Protein energy malnutrition. Family planning utilization decreases the risk of stunting and underweight. Feeding practices (pre-lacteal feeding and complementary feeding practice) were also related to undernutrition. Thus, nutritional intervention program in Bule Hora district in Ethiopia should focus on these factors.