Background Despite of the global efforts undertaken to improve nutrition, malnutrition still continues to be a serious public health concern. Malnutrition in its various forms has been closely associated to major causes of illness, disability and death. Malnutrition in the form of childhood stunting has therefore been identified as a significant hindrance to human development. The aim of this study was to assess the nutritional status of children aged 6–59 months and determine factors associated with a high prevalence of stunting (48%) among children in Kabale district. Methodology A cross sectional study was conducted among 640 children, aged 6–59 months selected using both simple random and systematic random sampling techniques. Interview administered questionnaires were used to collect household data whereas anthropometric data was collected using height boards, digital weighing scales and Mid Upper Arm Circumference (MUAC) Tapes. Nutrition status data was analyzed using ENA for SMART, 2011 and then exported to STATA version 12.0 for further analysis. Results The overall prevalence of stunting among children 6–59 months was 41.1%. Factors independently associated with stunting included; age of the child (children in the age category of 36-47 months APOR = 0.38; 95% CI 0.18–0.79 and those in the age category of 24-35 months APOR = 0.42; 95% CI 0.19–0.88), major source of food for the household that is children from households in which mothers indicated market as the major source of food (APOR = 0.67; 95% CI 0.48–0.94) and disposal of child stool that is children whose stool was put/ rinsed in a latrine (APOR = 0.41; 95% CI: 0.23–0.74) as well as those that whose stool was thrown in garbage (APOR = 0.29; 95% CI: 0.12–0.72). Conclusion The prevalence of stunting among children aged 6–59 months in Kabale district was high. Practices/ factors independently associated with stunting among children aged 6–59 months included; age of the child, major source of food for the household and disposal of child stool. Addressing these factors requires a proper mix of both community and health based interventions. There is also need to strengthen on strategies for reducing stunting like; sanitation and hygiene as well as food and nutrition security within rural households.
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