A new in vivo model for studying brain metabolic and hemodynamic oscillatory phenomena during ischemia is described. In this model, acute or chronic occlusion of one or two carotid arteries in the rat is performed. Due to the partial ischemia developed, oscillations in the level of intramitochondrial pyridine nucleotides (NADH) as well as flavoproteins (Fp) were recorded from the brain by monitoring the fluorescence of these respiratory chain components. The two fluorescent signals (NADH and Fp) were measured by using the time sharing or DC fluorometer/reflectometer. The changes in the reflected light at the excitation wavelengths (366 and 450 nm) were recorded simultaneously. Bilateral carotid artery occlusion induced immediate oscillations (6–9 waves per min) in the mitochondrial redox state as well as in tissue blood volume in both hemispheres. To verify the accuracy of the NADH monitoring system, including the correction technique for hemodynamic and other artifacts, we used the intracarotid artery saline bolus injection approach. The results could be summarized as follows: (1) unilateral carotid artery occlusion resulted in delayed development of oscillations, particularly in the ipsilateral hemisphere; (2) the oscillation phenomenon was reversible if recirculation restarted within 5 min. Occlusion for more than 30 min resulted in irreversible oscillations; (3) the oscillation appearances and intensities were affected by various physiological conditions. Vasoconstriction, induced by hyperoxia, stimulated the oscillations while vasodilation, induced by hypercapnia, depressed them. Anoxia, hypoxia, and spreading depression (50) abolished the oscillations. Glucose injection was not effective. Anesthesia under certain conditions enhanced the oscillations; (4) a clear phase difference was recorded between blood volume (R signal) and NADH redox state (F signal) waves; (5) analysis by phase relationship showed that the oscillations in various locations on the same hemisphere or between hemispheres appeared at different timings, suggesting a local oscillator. Using laser Doppler flowmetryLaser Doppler flowmetry (LDF) simultaneously with NADH redox state and ion selective extracellular K+ and Ca2+ electrodes, it was found that the mitochondrial oscillations in the NADH redox state were inversely correlated to tissue blood flow and volume. No correlation was found between the K+ and Ca2+ levels and the metabolic and hemodynamic oscillations, excluding the possibility that membrane pump activity (Na+/K+-ATPase or Ca2+-ATPase) are the oscillators. It was concluded that the metabolic oscillations recorded under ischemic conditions were dependent on local changes in blood supply as evaluated by blood flow and volume changes and pO2 level measurements. These oscillations in O2 supply led to the intramitochondrial oscillations of the NADH and Fp components of the chain.