Malnutrition among children is prevalent in almost all the states in India. This study assesses the extent and causes of malnutrition in two eastern Indian states with similar climates, namely West Bengal and Assam, using data from the National Family Health Survey 1998–99 (NFHS-2). The three indices of malnutrition taken for analysis are weight-for-height (WHZ), height-for-age (HAZ) and weight-for-age (WAZ). These are assumed to depend on birth order, preceding birth interval, parent’s educational status, working status of the mother, mother’s age at delivery of the children, source of drinking water, toilet facilities and standard of living of the household. Logistic regression was carried out separately for each of the three indices on the explanatory variables for both the states. It was found that not all variables are equally important in determining whether a baby is underweight, or suffering from acute or chronic malnutrition. Also, the importance of variables is not the same in the two states. It was observed that the coefficients associated with the variables in determining weight-for-height are not significant compared with those for weight-for-age and height-for-age.