There is empirical evidence at the national level that suggests the 1999 Indonesian economic crisis impact was very heterogeneous both between urban and rural areas and across regions. A cross sectional study of the nutritional status of children and its determinants was performed in urban poor areas of Jakarta, and rural areas of Banggai in Central Sulawesi, and Alor-Rote in East Nusa Tenggara. Two-stage cluster sampling was used to obtain 1078 households with under-five children in the urban poor area of Jakarta, and 262 and 631 households with under-five children each for the rural areas of Banggai and Alor-Rote, respectively. Data collection for both studies was performed from January 1999 to June 2001. The study shows that wasting affected more children in the urban poor areas of Jakarta than in the other study areas. On the other hand, stunting and anemia were significantly more severe among children 6-59 months of age in the rural area of Alor-Rote compared to the other study areas. The high prevalence of infectious diseases was significantly related to the higher prevalence of wasting in the study areas of Jakarta and Banggai, and also significantly related to the higher prevalence of stunting and anemia in the study area of Alor-Rote. To avert this kind of health impact of a economic downturn, there is a need to improve the nutritional and health status of under-five children and their mothers through the existing health care system, provide basic health services and improve the capacity of health staff across Indonesia as part of the decentralization process.