Malnutrition remains one of the most common causes of morbidity and mortality among children throughout the world. This study aimed to assess prevalence of malnutrition and associated factors among children aged 6–59 months in Damot Gale, South Ethiopia.

A community based cross sectional study was conducted on 398 children aged 6–59 months in the Damot Gale district. A two-stage cluster sample design was used to select kebele and households. Anthropometric measurements and structured questionnaires were used to collect data. Bivariate and multivariate logistic regression was done by using SPSS version 20.

The results of this study indicated that 27.6% of children were under-weight and 9% were wasted. Being male (AOR: 1.90; 95% CI: (1.10–3.32), children with shorter birth interval (AOR:2.89;95% CI: (1.23–6.80), children who had sickness some times for past 2 weeks (AOR:0.42; 95% CI:(0.10–0.93) and children whose mothers attended ANC (AOR:0.29; 95% CI: (0.16–0.52) were associated with underweight. Children whose mother’s main occupation was non-farm (AOR: 7.06;95% CI: (1.31–38.21), presence of diarrhea (AOR:39.5, 95% CI: (13.68–114.30), and children whose mothers attended ANC (AOR:0.18,95% CI: (0 .18 (0.07–0.45) were associated with wasting.

The prevalence of malnutrition in the study area was high. Health extension workers and stakeholders should give due concern on promotion of proper nutrition in the community.