In spite of favourable natural and human resource capacity, malnutrition remains an important health and welfare problem in Uganda especially among children below 5 years. Western Uganda has persistently registered highest levels of childhood malnutrition despite being referred to as “the food basket” of the country. This study sought to establish the causes of persistent child undernutrition to guide design of effective nutritional policies and interventions. This was a cross-sectional study that used both quantitative and qualitative methods. Multistage random sampling and stratified sampling were used to select study areas and households with children 6–59 months, respectively. Stunting levels were determined using anthropometric measurements of height-for-age using the US National Center for Health Statistics (NCHS) Reference Standards, which were approved for use in developing countries by the World Health Organization (WHO). The main causes of malnutrition were determined by logistic regression analysis. Almost half (46%) of children below 5 years were stunted, which is comparable to national prevalence of 47.8% for Western Uganda and this is unacceptably high. The major causes of stunting at (p =0.05) were improper health and sanitation, poor child feeding practices, poor access to appropriate knowledge for health and nutrition, poor socio-economic variables of access to food, type of employment, distance to main roads and markets, housing facility, income flow regime, gender disparities and access to fuel for cooking. Overall, there is low intake of animal protein and generally constrained access to adequate amount of food required for normal growth and development. At multivariate level, the main risk factors included; lack of information on child health feeding, socio-economic capacity of household, poor hygiene practices, and preparation of special foods for children. Results suggest that more emphasis needs to be put on community nutrition and health education with a focus on diet, hygiene, sanitation, social-economic and livelihood programs, improvement of health care services and diversification of interventions especially into poverty alleviation programs with a nutrition focus.