ObjectiveThe double burden of malnutrition affects many low and middle-income countries. This study aimed to: a) determine temporal trends in the prevalence of underweight, stunting, and at risk of overweight/ overweight or obesity in Indonesian children aged 2.0–4.9 years; and b) examine associated risk factors.DesignA repeated cross-sectional survey. This is a secondary data analysis of waves 1, 2, 3, and 4 (1993, 1997, 2000, and 2007) of the Indonesian Family Life Survey, which includes 13 out of 27 provinces in Indonesia. Height, weight and BMI were expressed as z-scores (2006 WHO Child Growth Standards). Weight-for-age-z-score <-2 was categorised as underweight, height-for-age-z-score <-2 as stunted, and BMI-z-score >+1, >+2, >+3 as at-risk, overweight and obese, respectively.ResultsThere are 938, 913, 939, and 1311 separate children in the 4 waves, respectively. The prevalence of stunting decreased significantly from waves 1 to 4 (from 50.8% to 36.7%), as did the prevalence of underweight (from 34.5% to 21.4%). The prevalence of ‘at-risk’/overweight/obesity increased from 10.3% to 16.5% (all P<0.01). Stunting and underweight were related to lower birth weight, being breastfed for 6 months or more, having parents who were underweight or had short stature, and mothers who never attended formal education. Stunting was also higher in rural areas. Being at-risk, or overweight/obese were closely related to being in the youngest age group (2–2·9 years) or male, having parents who were overweight/obese or having fathers with university education.ConclusionsThe double burden of malnutrition occurs in Indonesian children. Development of policy to combine the management of chronic under-nutrition and over-nutrition is required.