Pituitary adenylate cyclase-activating polypeptide (PACAP) has been shown to be a potent neuroprotective agent in global and focal ischemia. We demonstrated that PACAP could cross the blood-brain barrier (BBB) by a saturable transport system, and a systemic administration of PACAP reduced the infarct induced by unilateral middle cerebral artery occlusion (MCAO). Therefore, we studied whether this transport system is affected by MCAO in the rat. The entry of PACAP38 into the brain was compared in five groups: control, 4, 6, 24, and 48 h after MCAO. [(125)I]PACAP38 was injected intravenously and serum and various brain regions were collected 3 min later. The rate of entry into the brain of PACAP38 was also determined. We showed that PACAP entered the rat brain via a rapid transport system when the BBB is intact. After transient (2 h) unilateral MCAO, all regions of the brain, showed a selective increase in the passage of PACAP38 across the BBB after 4 h after the occlusion, which was not related to any generalized change in the permeability of the BBB, as measured with albumin. A significant decrease in the amount of PACAP38 entering the brain was observed in the 6- and 24-h groups, but it returned to the baseline level in the 48-h group. These results suggest that focal cerebral ischemia can selectively modify the passage of PACAP38 across the BBB, in both damaged and undamaged sides of the brain, and that these changes in influx are not solely due to the disruption of BBB. These findings imply the necessity of adjusting the dose of intravenously administered PACAP38 in order to maximize its therapeutic effect on the brain damage resulting from focal ischemia