Background: Severe acute malnutrition is one of the major killers of under five children in developing countries including Ethiopia. However, little information is known about the determinant factors of severe acute malnutrition. Hence this study identified the determinants of severe acute malnutrition in Shashogo woreda, Southern Ethiopia. Methods: An age matched community based case control study was conducted from February 20 to march 30, 2014 in 12 randomly selected rural kebeles of the Shashogo district, southern Ethiopia. The cases were 108 severely malnourished children under the age of five and the controls (n=108) were children without malnutrition recruited concurrently from under five children of the same kebele. Data was collected by face to face interview using structured questionnaire and the anthropometric measurements of the children was taken using standard procedures. Descriptive and summary statistics was done. Bivariate and multivariate analysis was done using conditional logistic regression on SPSS version 20.0 and Epi info version 7 software in order to determine factors associated with severe acute malnutrition. Result: Multivariate analysis with conditional logistic regression revealed that severe acute malnutrition was associated with maternal illiteracy (AOR=8.683, 95% CI 2.668 – 28.26), lack of maternal autonomy in decision making (AOR = 3.46, 95% CI 1.272 – 9.414), diarrhea 2 weeks preceding the survey (AOR = 4.13, 95% CI 1.34– 11.47), sub optimal frequency of complementary feeding (AOR = 3.21, 95% CI 1.63 – 9.33) and visit to health institution after 24 hours of the onset of symptoms for sick child (AOR=3.95, 95% CI 1.465 – 10.647) after the effects of other significant variables were controlled. Conclusion and Recommendation: The findings of this study have confirmed the association of severe acute malnutrition with maternal education, maternal autonomy in decision making and inappropriate infant and young child caring practices. To reduce childhood malnutrition due emphasis should be given in empowering women and improving the knowledge and practice of parents on appropriate infant and young child caring practices.