Maternal deprivation (MD) leads to a variety of behavioral changes in rats which closely resemble the symptoms of schizophrenia in humans. With the aim to investigate the morphological changes which underlie the behavioral insults in this experimental paradigm we exposed 9-day-old Wistar rats to a 24 h MD. At the period of young adulthood rats were sacrificed for morphometric analysis and their brains were compared to the control group. Rats exposed to MD had a decrease in hippocampal volume (71 percent of the control value) as well as a decrease in the size of pyramidal (62 percent of the control) and granular (60 percent of the control) cell layers. Also, there was a decrease in the thickness of the prefrontal, retrosplenial and motor cortex compared to the control group. Analysis of the density of NeuN-immunolabeled neurons revealed a reduction in retrosplenial and prefrontal cortex (70 percent and 81 percent of the control, respectively), while there was no difference in the motor cortex. Western blot analysis confirmed a decrease in NeuN expression in the MD group compared to the control rat brain homogenates. The results of this study show that early stress in life has a long-term effect on the morphology of cognitive brain regions, most probably due to the loss of neurons during postnatal development and further contributes to our understanding of the effects of maternal separation on brain development.