Early life experiences have strong influences on brain programming and can affect eating behavior control and body weight later in life. However, there is no consensus about the relationship between neonatal stress and feeding behavior. We evaluated whether maternal deprivation (MD) and maternal separation (MS) alter body weight and appetite using standard rat chow consumption and palatable food. Also, we evaluated anxiety and the expression of the leptin receptor, neuropeptides POMC, CART, NPY in the hypothalamus, as well as the serotoninergic system in the amygdala and hypothalamus as possible modulators of these behaviors. We found a decrease in standard rat chow consumption in MD. However, both neonatal stress protocols increased the consumption of palatable food and led to anxiogenic behavior in male animals. MD led to decreased hypothalamic POMC levels in adult males. Serotonin in the hypothalamus was decreased by both stress models in males and females. In the amygdala, MS decreased serotonin levels while MD increased its metabolite levels. We observed that males are more vulnerable and females are more resilient to the effects of neonatal stress on anxiety-like behavior, as well as on food consumption and on the central changes observed. These data together add support to the concept that the early environment contributes to the development of eating disorders later in life.