Several studies using animal models have suggested that the effects of nutritional insult on the developing brain are long-lasting and lead to permanent deficits in learning and behavior. Malnutrition can refer to the availability of all the nutrients but in insufficient quantities or it may imply that one or more of essential nutrients is either missing or is present, but in the wrong proportions in the diet. The hypothesis addressed in this study is that different domains of cognitive functioning can be affected by malnutrition and this can be related to the type of nutritional deficiency that the brain has been exposed to during development. To study the effect of nutritional deprivation during brain development, a paradigm of maternal malnutrition during the period of gestation and lactation was used and its effects were studied on the F1 offspring using Swiss albino mice. Three different types of malnutrition were used, that involve, caloric restriction, inadequate amount of protein in the diet and condition of low iron content. Our results show that the domain of spatial memory affected in the F1 generation depended on the kind of malnutrition that the mother was subjected to. Further our study shows that although hippocampal volume was reduced in all F1 pups, hippocampal subregions of the F1 animals were differentially vulnerable depending on type of malnutrition that the mother was subjected to. These results highlight the importance of qualifying the kind of malnutrition that is suffered by the mother during the period of gestation and lactation as it has consequences for the cognitive domain affected in the offspring. Awareness of this should inform prevention strategies in trying to reverse the effects of adverse maternal nutrition during critical periods in brain development.