The children living in rural areas of India disproportionately suffer from malnutrition compared with their urban counterparts. The present article analyses the individual, household, community and programme factors on nutritional status of children in rural India. Additionally, we consider the random variances at village and state levels after introducing various observed individual-, household- and programme-level characteristics in the model. A multilevel model is conducted using data from the National Family and Health Survey 2. The results show that maternal characteristics, such as socio-economic and behavioural factors, are more influential in determining childhood nutritional status than the prevalence of programme factors. Also, it was found that individual factors show evidence of state- and village-level clustering of malnutrition.