Background: Malnutrition is the widely known nutritional disorder and one of the leading causes of morbidity and mortality among children in developing countries like Ethiopia. About 50% of under-nutrition around the world is associated with infections caused by unsafe water, inadequate sanitation or insufficient hygiene. However, there are limited available data which associate water supply, sanitation and hygiene practices and childhood malnutrition in Ethiopia particularly in the study area. Therefore, the objective of this study was designed to examine the association of water supply, sanitation and hygiene interventions and childhood malnutrition.Methods: Case-control study design was conducted from December 2018 to January 2019 Kersa and Omo Nada districts of Jimma Zone, Southwest Ethiopia. Randomly 126 cases and 252 controls were selected from the malnourished children and normal children, respectively. A pretested, structured, interviewer-administered questionnaire was used. Bivariate and multivariable logistic regression analyses were used to identify the study variables associated with childhood malnutrition and to adjust for confounders. The crude and adjusted odds ratios with 95% confidence interval was calculated to assess the level of significance and reported for each confounding variable.Results: The results of this study showed that children living with mothers/caregivers lack of formal education were found to have 57% times less likely developed malnourished, compared to those living with mother/caregiver who attended secondary and above (AOR = 0.57; 95% CI: 0.26-1.24). The odds of having malnutrition were increased among children who were breastfed after one hour of birth (AOR=2.60; 95% CI: 1.02-6.65) and children who had diarrhea (AOR=9.50; 95% CI: 5.19-17.36).Collecting water from a distance of less than/equal to one kilometer (AOR=2.52; 95% CI: 0.56-11.39), defecating in open pit(AOR=1.33; 95% CI: 0.62-2.83),under-five children open field defecation practices (AOR=1.17; 95% CI: 0.42-3.23) and lack of hand washing at critical times (AOR=2.38; 95% CI: 1.07-5.29) were positively associated with childhood malnutrition. Conclusion: We conclude that improvement in the initiation of breastfeeding within one hour, diarrhea prevention, use of improved latrine and hand washing at critical times is needed to improve the nutritional status of children.