Cyclooxygenase-2 (COX-2) and presenilin (PSEN) 1 and 2 genes are regulated during development as well as in pathological conditions associated to hypoxia. In this study, we investigated their patterns of expression during the first 2 weeks of postnatal life in a rat model of moderate global perinatal asphyxia that we have previously reported to be characterized by early oxidative stress and delayed behavioral alterations. In the hippocampus, global perinatal asphyxia induced an early up-regulation COX-2 mRNA (postnatal day, pnd, 1), which preceded those of PSEN 1 and 2 genes, observed at pnd 4. At pnd 11, the expression of all three genes was decreased compared to control animals. In addition, we analyzed the expression of the scavenging enzymes catalase, copper/zinc- and manganese-superoxide dismutase. As for COX-2, the three enzymes were up-regulated in the hippocampus at pnd 1 and returned at or below baseline by pnd 4. In the cortex, only PSEN 1 and 2 showed a moderate up-regulation at pnd 1 followed by a down-regulation at pnd 11. These findings suggest that moderate perinatal hypoxic episodes are associated with a dysregulation of the several genes involved in brain development and anti-oxidant defenses, which follows a rapid and transient oxidative stress. Such alterations are particularly evident in the hippocampus and could represent an adaptive response to the hypoxic condition. The delayed down-regulation of the scavenging enzymes could set the ground for brain damage and delayed behavioral alterations and further support the potential benefit of early anti-oxidant treatments in a short therapeutic window soon after birth.