The Sundanese inhabiting West Java, the second largest ethnic group in Indonesia, are characterized by a high prevalence of child malnutrition, together with high fertility. Based on an anthropometric measurement and interview survey of 310 children aged 5–12 years in a rural Sundanese village, this study examined the relative significance of the effects of eight biological, eight socioeconomic status (SES) and four health behavioural factors on their Z scores for height-for-age (HAZ) and weight-for-age (WAZ) in particular. Three biological factors, i.e. birth interval, birth weight and mother’s body weight, and one SES factor, i.e. mother’s occupation, were selected as the predictors of the two Z scores by regression analysis, indicating more significant effects of the biological factors than the other factors. This pattern is judged to occur in less-developed and high-fertility populations. Since these two Z scores were worse in the subject children than in the under-5-year-old children from the same village, more attention should be paid to the long-lasting effects of birth-related biological factors up to pre-adolescent ages, as an insufficient nutritional status tends to damage growth and health in adolescence and adulthood.