Background; The prevalence of stunting and helminthiasis among children in Uganda and Sub-Saharan Africa is still high and if Uganda is to achieve the food-related Sustainable Development Goals (SDGs), it must urgently invest in improving nutrition and sanitation . In a food rich area like Bushenyi, chronic under nutrition could be due to several other factors than mere scarcity of food. This study was carried out to determine the prevalence and socio-clinical factors responsible for chronic under nutrition (stunting) among pre-school children aged 1-5 years in selected Health facilities in Bushenyi district.Methods: A cross-sectional study on prevalence of chronic under nutrition (stunting) and related factors among children 1-5 years. Data was collected using a pre-tested questionnaire and using anthropometric measurements (height/ length), and standard laboratory procedures (stool analysis for eggs of soil transmitted helminthes), then recorded in a data card. Stool samples were collected from 206 children and analyzed for soil transmitted helminthes’ eggs using Formol-ether concentration method. Results: Majority were female (59.7%) aged above two years, with a median age of 2.1 years (IQR= 1.6-2.8). Most children (92.2%) stayed with their parents and resided within Bushenyi municipality (54.9%). Many lived within an extended family (52.4%) and 92.2% had been brought to the health center by their parents who were married (71.8%). children who were likely to be stunted were those who drank unboiled water (aPR=1.21, 95%CI 1.10-1.34) and were exclusively breastfed (aPR=1.35, 95% CI 1.11-1.65). The proportion of children with stunting was 89.3% (95%CI 83.3-92.9).Although most of the children were dewormed twice a year (64.1%), they did not wash their hands after using the toilet and before eating (84.6%). Furthermore, a majority of them (76.2%) rarely wore shoes. Almost all of the caregivers (96.1%) reported that they had never received any form of education on how to feed their children. However, many of the children (74.3%) had or were being exclusively breastfed and half of them (50.5%) drank boiled water. A few of the children (10.7%) were infested with soil transmitted helminthesConclusion: The prevalence of chronic malnutrition is in Bushenyi district is very high despite the abundance of food. This is due to several factors including parents’/care takers’ low knowledge. The study therefore recommends intensive continuous education on proper nutrition of preschool children and its benefits to the communities in Bushenyi District.Trial registration: Not applicable.