Melatonin (Mel) has strong antioxidant properties since it is a direct scavenger of oxygen-based free radicals and related species. The main aim of this study is to show whether the effects of Mel can prevent the potential adverse effects of diclofenac sodium (DS), used as a non-steroidal anti-inflammatory drug (NSAID) during the prenatal period, on the newborn experimental rat brain tissues using stereological methods Twenty-four male 12-week old Wistar albino rats were used. The study involved four groups (each containing six rats), those exposed, during the prenatal period, to saline 1ml/kg (Saline group), to diclofenac sodium 3.6mg/kg (DS group), or to diclofenac sodium+melatonin 50mg/kg (DS+Mel group), and a control group (Cont group). At the end of the experiment, the brains were removed from the cranium for histological and stereological analyses. Cell loss in the hippocampus exposed to DS was observed compared to the Cont group (p<0.01), and a similar side-effect was also seen in the Saline group (p<0.01). However, there was no significant difference in cell numbers between the Cont and DS+Mel groups (p>0.05). These results suggest that exposure to DS during pregnancy causes a decrease in the number of cells in the hippocampus and dentate gyrus in the postnatal period. Using Mel, a neuroprotective agent, reduced the toxic effects of DS.