Indonesia is currently facing the double burden of malnutrition. While undernutrition is still a major public health problem, the prevalence of overnutrition is increasing. The objective of the South East Asian Nutrition Survey (SEANUTS) was to provide up-to-date data on nutritional status, food consumption and biochemical parameters related to nutrition for children aged 0·5–12 years. The SEANUTS study in Indonesia was conducted in a nationwide representative sample of 7·211 children using multistage cluster sampling based on probability proportional to size, stratified for geographical location, in forty-eight out of 440 districts/cities. The results show that the growth (weight for age, height for age, weight for height and BMI for age) of Indonesian pre-school- and school-aged children is below the WHO standards. The older the children, the more the deviation from the WHO standard curves. Underweight was more prevalent in rural areas (28·9 v. 19·2 %) and overweight/obesity was observed to be more widespread in urban areas (5·6 v. 3·2 %). The prevalence varied with age groups and sexes. The overall prevalence of stunting was 25·2 and 39·2 % in urban and rural areas, respectively. The prevalence of anaemia was nearly 55 % in children aged 0·5–1·9 years and ranged from 10·6 to 15·5 % in children aged 2–12 years. Fe deficiency was observed in 4·1–8·8 % of the children. The percentage of children with dietary intakes of energy, protein, and vitamins A and C below the Indonesian RDA was high and differed across urban and rural areas and age groups.