Childhood underweight is a problem being faced by rural black South African populations but little is known about its risk factors. The aim of this study was to investigate the risk factors related to childhood underweight in rural black South African children within the area known as Ellisras. A cross-sectional study was conducted as part of the ongoing Ellisras Longitudinal Study. The current study comprised a total of 1 811 pre-primary and primary school children (934 males and 877 females) aged between five and 16 years. The chi-squared automatic interaction detection (CHAID) decision tree model was used to identify factors and determine their relationships with childhood underweight. A total of 1 811 children were involved in the study, of whom about 81% were severely underweight. The CHAID model showed that the variables: nutrition, age group, gender and school level were the four main predicting variables affecting childhood underweight. Hypertension was not significantly associated with childhood underweight. The prevalence of childhood underweight was found to be high in children aged between five and 16 years. To address this problem, well-thought-out intervention systems are need.