Cardiovascular parameters such as arterial blood pressure (ABP) and heart rate display pronounced circadian variation. The present study was performed to detect whether there is a circadian periodicity in the regulation of cerebral perfusion. Normotensive Sprague Dawley rats (SDR, appr. 15 weeks old) and hypertensive (mREN2)27 transgenic rats (TGR, approximately 12 weeks old) were equipped in the abdominal aorta with a blood pressure sensor coupled to a telemetry system for continuous recording of arterial blood pressure, heart rate, and locomotor activity. Five to twelve days later, a laser-Doppler flow (LDF) probe was attached to the skull by means of a guiding device to measure changes of brain cortical blood flow (CBF). After recovery from anesthesia, measurements were taken for 3 - 4 days. The time series were analyzed with respect to the midline estimating statistic of rhythm (MESOR, i.e. mean value of a periodic event after fitting to a cosinus function), amplitude, and acrophase (i.e. the phase angle which corresponds to the peak of a given period) of the 24 h period. The LDF signal displayed a significant circadian rhythm with the peak occurring around midnight in both, SDR and TGR, despite the inverse periodicity of the ABP in TGR. This finding suggests independence of LDF periodicity from ABP regulation. Furthermore, the acrophase of the LDF was consistently found prior to that of the activity. From the present data it is concluded that there is a circadian periodicity in the regulation of cerebral perfusion which is independent from circadian changes of ABP and probably also from locomotor activity. The presence of a circadian periodicity in the CBF may have implications for the occurrence of diurnal alterations of cerebrovascular events observed in humans.