Background: Malnutrition is defined as a pathological state resulting from a relative or absolute deficiency or excess of one or more essential nutrients. Weight for age, height for age and weight for height are usually used to describe the nutritional status of children. The present study was done to compare the anthropometric measurements of children attending urban and rural anganwadi centres.Methods: A cross sectional study was carried out in children aged three to six years attending 34 anganwadi centres of a coastal district of Karnataka. Anthropometric measurements like height, weight and mid arm circumference was measured using standard methods. Malnutrition was assessed based on WHO z scores. Statistical analysis used: Data was expressed in Percentages and frequencies. Comparison of anthropometric measurements were done using chi square analysis.Results: 25.5% of the children attending urban anganwadis were underweight, 10% severely underweight, 15.5% stunted, 2.5% severely stunted, 24% wasted and 8.5% severely wasted. 18.5% of children attending rural anganwadis were underweight, 6.8% severely underweight, 11.8% stunted, 3.2% severely stunted, 15.2% wasted and 4.5% were severely wasted. The prevalence of wasting was significantly higher (p=0.006) in children attending urban anganwadi centres compared to rural centres.Conclusions: Urban anganwadis had a higher prevalence of underweight, stunting and wasting. Underweight and stunting was higher in females compared to males whereas wasting was found almost equally in both the genders.