Introduction: Malnutrition is one of the leading causes of childhood death. In the southern provinces of Thailand that are encountering a civil conflict, the extent of malnutrition among young children has not been adequately reported. Methods: A cross-sectional study was undertaken to assess the nutritional status of children aged 2-5 years enrolled in early childhood development centres (ECDC) in Pattani Province. A total of 112 ECDCs were randomly selected and 871 children who met the inclusion criteria were recruited. Anthropometric measurements were taken and nutritional status determined according to World Health Organization (2006) growth standards. Statistical analyses of nutritional indicators, namely wasting, stunting, underweight and Composite Index of Anthropometric Failure (CIAF) across sociodemographic variables were carried out. Binary logistic regression models, based on the different nutritional indicators, were used to determine the relationships between undernutrition status and associated factors. Results: Prevalence of wasting (7.7%), stunting (19.6%) and underweight (16.8%) were determined. Based on CIAF, 27.4% of the children were undernourished. Logistic regression odds showed that prevalence of all forms of undernutrition was statistically independent of sex and place of residence. Religion was associated with all four indicators of undernutrition. Stunting was associated with child’s age and religion, while underweight and CIAF were associated with the child’s age, religion and mother’s occupation. Conclusion: Prevalence of undernutrition was estimated to be high in comparison with the national average figure. The study findings highlighted the need for more effective nutrition promotion activities to alleviate undernutrition problems among young children in Pattani Province.