This study aimed to assess the determinants of under nutrition among under-two year old children of rural Bangladesh. The data of the National Nutrition Program baseline survey conducted in 2004 was analysed, which included 8,885 under-two children and their mothers. Among the children studied, 41%, 35% and 18% were stunted, underweight, and wasted; and 16%, 11.5% and 3% were severely-stunted, -underweight, and –wasted, respectively. Multivariate analysis revealed that undernourished children were less likely to be female and having received measles vaccination, more likely to have suffered from diarrhea in the previous two weeks, and more likely to have older- (>30 years), shorter- (<145 cm), undernourished- (BMI ≤18.5 kg/m2) and illiterate/less educated mother. Children with moderate stunting and underweight were more likely to reside in households with un-hygienic toilet. Children with all forms of under nutrition were more often from families with lowest quintile of asset index. The identified associated/risk factors can be used for designing and targeting preventive programs for undernutrition.