Aging affects different parts of the brain structure and function. These changes are associated with several age-related emotional alterations like anxiety that is regulated by the amygdala and medial prefrontal cortex (mPFC). Thus, this study aimed to explore the effects of aging on the morphology changes in these regions. Twenty male Wistar rats were assigned to young and old groups. The anxiety level was evaluated by elevated plus-maze. Then, their brains were removed, fixed, cut, and stained with Cresyl Violet or Golgi-Cox. In addition to the estimation of stereological parameters, dendrite complexity, and spatial distribution of the neurons in the mPFC and amygdala were evaluated. Aging increased the medial amygdala volume and its total number of neurons, but it did not have a significant effect on these parameters in the mPFC. Furthermore, the size of the neurons in the mPFC increased, whereas the total length of the dendrite and its complexity significantly decreased with aging in this structure and increased in the amygdala. Although aging did not significantly change the dendritic spine density in both regions, old rats showed a more mature spine in the mPFC and more anxiety-like behavior. In conclusion, the increase of anxiety in the old individuals could be attributed to structural changes in the morphology of the dendrite and neuron and its spatial distribution in the mPFC and amygdala. The findings of this study partly support this hypothesis. © 2020 The Author(s).