Prenatal stress has been shown to disturb neonatal rat brain development. The astroglial-specific neurotrophic factor S100B is known to play an important role in normal brain development. In the present study, we investigated the effects of prenatal stress on S100B concentrations in the hippocampus of 1-day-old Fischer 344 rats. Overall, prenatal stress resulted in a 25% reduction in hippocampal S100B content. Further, male hippocampal S100B content was negatively correlated with plasma corticosterone levels. Positive correlations were found between female S100B levels and fetal growth, and hippocampal brain-derived neurotrophic factor content. In conclusion, the observed reduction in neonatal hippocampal S100B levels, as a consequence of prenatal stress, may be involved in affecting postnatal brain development.