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This was a cross sectional analytical community based study to assess the prevalence and factors associated with malnutrition among children aged 6-59 months in Jubek state, South Sudan. Anthropometric measurements including weight, length/ height, mid upper arm circumference (MUAC) were taken and HIV test. The equipment used included: WHO recommended MUAC tape for 6months to 59 months old children, digital weighing scale (SECA) and portable Stadiometers. Data were collected from 396 children using a pretested semi- structured questionnaire. The analysis of this study revealed that, 32.2%, 28.2% and 32.3% of children were stunted, wasted and underweight respectively. The main associated factors of stunting were age older than one year (p= 0.004), children from households who were renting their houses and children who defecate in open spaces with no latrine at their homes (p= 0.015). Underweight was associated with child's age (p= 0.001), loss of appetite (p=<0.001), children who ate from own plate (p=0.001) and children who didn't consume meat (p=0.007).