Growth and development events are observed in all organisms and can be modified by exogenous factors such as nutritional changes. Drastic morphological and functional alterations may occur during a vulnerable stage of development. The aim of this study was to investigate if malnutrition and/or fluoxetine neonatal treatment program alterations in heart morphology during the postnatal period. The sample consisted of 48 albino Wistar male rats. The rats were divided into two groups: nourished and malnourished. Pharmacologic manipulation was performed during the suckling period. The animals of each group were divided into two subgroups: saline-nourished and saline-malnourished, treated with sodium chloride solution, and fluoxetine-nourished and fluoxetine-malnourished, treated with fluoxetine. Half of the individuals in each subgroup were weighed and sacrificed on day 30 and the other half on day 71. Myocardial perfusion was performed and the heart subsequently weighed. The ventricles were cross-sectioned into two parts, which were fixed, dehydrated and sectioned. There were differences in body weight, heart weight, cross-sectional area and perimeter of the heart and in the cross-sectional area and perimeter of the cardiac cells among the groups at the different ages. Malnutrition appears to program alterations in heart morphology. However, malnourished animals that had undergone drug treatment did not exhibit the same changes.