Objectives: This representative, cross-sectional study conducted in Kabarole District, Western Uganda, determined the nutritional status of children 6–59 months of age and established a trend in the childhood stunting rates. Methods: A multi-stage random cluster sampling was performed to select 322 children and their principal caregivers. Anthropometric measurements were taken from the children and compared with a reference population and the children’s principle caregivers were interviewed. Results: Childhood stunting was high with 43.0% of all children having a z-score of less than or equal to -2. Predictive factors for stunting were a low economic status of the household, poor health of the child’s caregiver, residence located at a long distance from a health unit and use of a contaminated water source. The comparison of our study results with an earlier nutritional study in Kabarole District revealed that there is an increasing trend of childhood stunting over the years of 28.0% [95% confidence interval (CI) 22.1–33.1%] in 1989 vs 43% (95% CI 37.6–48.8%) in 2006 and that stunting rates in Kabarole District were much higher compared to national data. Conclusion: The high stunting rates in children and the increasing trend in stunting needs further investigations. It should also be determined why stunting rates in children in Kabarole District are much higher than the national average. There is a need for better nutritional interventions as part of the district’s public health programs.