Reduced oxygen supply during the perinatal period often leads to acquired neonatal brain damage. So far, there are no reliable markers available to assess hypoxic cerebral damage and resulting prognosis during the immediate postnatal period. Thus, we aimed to determine whether the hypoxia-inducible transcription factors (HIF-1 and HIF-2) and/or their target genes in the placenta represent reliable indicators of hypoxic distress of the developing brain during systemic hypoxia at the end of gestation. To this end, pregnant mice were exposed to systemic hypoxia (FiO2 6%, 6 h) at gestational day 20. This hypoxic exposure significantly increased HIF-1 and HIF-2 protein levels in brains and placentas. Compared to controls, an increase of HIF-1-immunoreactive neurons and HIF-2-positive glial cells and vascular endothelial cells was observed in hypoxic cerebral cortex and hippocampus. In placenta, HIF-1 and HIF-2 were expressed in labyrinthine layer with increased staining intensity during hypoxia compared to normoxia. Significant up-regulation of VEGF mRNA and protein in brain and placenta as well as erythropoietin protein in placenta indicated activity of the HIF system upon fetal hypoxia. Notably, hypoxia did not affect expression of the HIF-target genes iNOS and GLUT-1. Taken together, at GD 20, systemic hypoxia led to up-regulation of HIF-’s in mouse brain that was temporally paralleled in placenta implying that both -subunits of HIF-1 and HIF-2 are indeed early markers of hypoxic distress in vivo. If our data reflects the situation in human, analysis of the placenta will allow early identification of the hypoxic brain distress occurring near birth.