A comparative analysis of the factors affecting the nutritional status of children under five years in Khulna and Sylhet divisions was undertaken. The Bangladesh Demographic and Health Survey data were used to identify and compare the socioeconomic, demograpic and environmental factors which had effect on the nutritional status of children in Khulna and Sylhet divisions. A total of 479 children from Khulna and 305 children Sylhet were weighed and measured for nutritional status and selected for this study. Two indicators, height for age, and weight for age, were analyzed. Childrens nutritional status is presented in mean Z scores. This report showed that the children in Sylhet division were more likely to be malnourished than to the children in Khulna division. The results from bivariate analysis showed that childrens nutritional status is significantly associated with parents education, and fathers occupation. Younger children were found to be less malnourishe compared to the older children and the association of age of child and duration of breastfeeding with children stunting and underweight was highly significant both in bivariate and multivariate analysis. Environmental factors affecting nutritional status of children are electricity supply at the households and hygienic sanitation facilities which were found to have significant influence on childrens nutrition in both the areas. When all the variables were included in the multivariate andlysis the number of variables which had significant relationship with height for age of children was reduced compared with the bivariate analysis. The general linear model showed highly significant difference between Khulna and Sylhet divisions and also in regard to the age of child, duration of breast feeding, having electricity supply at households and obtain and ability to read newspapers. This indicates that other variables had their effect through these explanatory variables on the nutritional status of children aged under five years in Khulna and Sylhet divisions. The R squared value explained 19 per cent of variation in the height for age (stunting) of children. Therefore further study is recommended for detecting the actual factors which affect the nutritional status of children in the two divisions.