South Sudan is the world's youngest nation which gained independence from Sudan on the 9th of July, 2011. Rates of acute malnutrition have been consistently higher in South Sudan than any other country in sub-Saharan Africa, more than twice the average reported for countries in Sub-Saharan Africa. This study sought to determine the prevalence and factors associated with malnutrition among children aged 6-59 months in Jubek State, South Sudan. Methods: This was a cross sectional analytical

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... ity based study to assess the prevalence and factors associated with malnutrition among children aged 6-59 months in Jubek State, South Sudan. Data was collected using a structured questionnaire from 396 children. Anthropometric measurements including weight, length/ height, mid upper arm circumference (MUAC) were taken and a blood sample by finger prick was removed for HIV test. The equipment which were used included: WHO recommended MUAC tape for 6months to 59 months old children, digital weighing scale (SECCA) and portable Stadiometers. Data were collected using a pretested semi-structured questionnaire. Results: 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). Male genders (p=0.022), households with two or more children aged zero to five years (0.010) not consuming vitamin A rich vegetable (p=0.002), diarrheal disease within two weeks prior to interview (p=0.006) and those from households with water sources other than piped (<0.001) were also associated with