Golden period that is often referred as the `window of opportunity' occurs in the first five years of life. This analyzed the role of the levels of observation that is compositional (individual) and contextual (household and primary health care sub district level) to the the status of malnutrition in Indonesia. The research was observational with cross-sectional design, using data Baseline Health Survey (Riskesdas) 2010 and Health Facility Survey (Rifaskes) 2011. The three levels of samples are individual children, households who have children, and health services in health centers at sub-district. Multilevel modelling analysis using logistic regression is applied using Stata program. The results of analysis concluded that the most role of contribution to malnutrition was at household level (42.5%), followed by the role of individual level (41.8 %) and health services at sub-district level (15.7%). At the individual level that contribute to malnutrition are inadequate protein-energy consumption (OR: 1.58), incomplete immunization (OR: 1.47) and not routine weighing (OR: 1.37). Children in the households with a condition: mother never graduated from junior high school, have children more than 3, and poor waste management 5.36 times risks of malnutrition. In the sub-district health center level, the variable whose role is making the report is not good, and children who live in these sub-district, 2.5 times as likely to experience malnutrition. In conclusion that the status of malnutrition in children under five years in Indonesia is determined by contextual factors, in addition to compositional factors.