The aim of this paper is to assess the spatial distribution of nutritional status of children of less than three years through Z-scores of weight-for-age, height-for-age and weight-for-height using data collected by the National Family Health Survey (NFHS-2, 1998–99), India. The nutritional status of pre-school children was regressed on different socio-demographic factors after eliminating the effect of age. The data show that there are gender differences and spatial variations in the nutritional status of children in India. Gender difference is not very pronounced and almost disappears when the effects of age and socio-demographic variables are removed. The spatial difference, especially the rural–urban difference, was found to be very large and decreased substantially when the effects of age and socioeconomic variables were removed. However, the differences were not close to zero. All the variables were found to affect significantly the nutritional status of children. However, the literacy of mothers did not affect height-for-age significantly. The weight-for-age and height-for-age scores showed a dismal picture of the health condition of children in almost all states in India. The worst affected states are Bihar, Madhya Pradesh, Orissa and Uttar Pradesh. Assam and Rajasthans are also lagging behind. Weight-for-height scores do not give a clear picture of state-wise variation. Goa, Kerala and Punjab are the three most developed states in India and also have the lowest percentages of underweight children according to the Z-scores. Along with these three states come the north-eastern states where women are well educated. Thus overall development, enhancement of level of education and low gender inequality are the key factors for improvement in the health status of Indian children.