Cerebral ischemia is caused by damaged blood supply to the brain, leading to an interruption in the oxygen balance of supply vs. demand. As a result, the impaired tissue suffers from various metabolic alterations, which lead to the formation of a new microenvironment in the ischemic tissue. Lack of oxygen to the brain interrupts the mitochondrial electron transport chain activity, resulting in a decrease of ATP synthesis and elevation of mitochondrial NADH levels. Due to its sensitivity to cellular oxygen levels, mitochondrial NADH serves as an indication to various pathological conditions in the tissue. When focal cerebral ischemia occurs, only a limited area in the brain suffers from a decrease in blood supply. The ischemic tissue suffers from a gradual injury, which spreads from severe damage in the central core area and onto moderate damage in peripheral areas known as penumbra. While the core displays severe lack of blood supply, the penumbra holds partial supply of blood, due to the existence of collateral blood vessels. Correspondingly, oxygen supply and mitochondrial function are more severe in the core compared to the penumbra. Studies show that focal ischemic damage can be reduced by inducing another form of a more moderate ischemia as ischemic preconditioning or ischemic postconditioning treatments. Ischemic preconditioning is based on the assumption that mild degree of ischemia increases the tolerance of the tissue when facing additional ischemic insult. Ischemic postconditioning is induced during the primary ischemic duration or at reperfusion and aims to reduce reperfusion injury. The aims of the current study include the evaluation of mitochondrial function and blood flow before, during and following different states of cerebral ischemia, with emphasis on focal cerebral ischemia. The study investigated the effects of ischemic duration on cerebral blood flow (CBF) and mitochondrial NADH in different regions of the ischemic brain. A comparison between mitochondrial function and CBF during focal cerebral ischemia compared to global partial cerebral ischemia was held. The study also examined the variability in outcomes of mitochondrial function and CBF that were examined following focal cerebral ischemia. In addition, the ability of the brain to function under metabolic challenges, which include oxygen deprivation and induced spreading depression (SD) waves, was examined. Finally, the study investigated the possibility of ischemia and reperfusion treatment using preconditioning and postconditioning ischemic procedures. Evaluation of mitochondrial function and the hemodynamic activity of the tissue was performed using a multisite multiparametric (MSMP) monitoring system, which combines NADH measurement using the fluorometric technique and CBF measurement using laser Doppler flowmetryLaser Doppler flowmetry (LDF), simultaneously and in real time in two regions of the brain. Focal ischemia was induced by middle cerebral artery occlusion (MCAO)—a common used mode of ischemic stroke. Global ischemia was induced by ligation of one or both carotid arteries. The results of the study introduce a continuous, multiparametric, in vivo and real-time monitoring of mitochondrial NADH and blood flow before, during and following cerebral ischemia. Results show that MCAO leads to reduction of tissue blood supply, accompanied by lack of oxygen and mitochondrial dysfunction. The hemodynamic and mitochondrial insult occurs in the hemisphere ipsilateral to the occluded artery. The ischemic lesion is gradual and spreads from severe damage in the core to moderate damage in the penumbra. Severity of mitochondrial and hemodynamic damage increases as ischemic duration increases, while the ability of the tissue to recuperate decreases. Study results demonstrate that after 24 h, transient focal ischemia leads to vast damage in the core alone, while permanent ischemia leads to equal damage to the core and the penumbra. The current study presents, for the first time, a comprehensive evaluation of different result profiles, which occur following a single model of focal ischemia. These profiles differ in CBF patterns, reperfusion reaction and survival of study animals. The wide variability in outcomes indicates the complexity of the MCAO model. Evaluation of this variability may assist other researchers using the same MCAO model as well as other models for focal ischemia. The current study presents a detailed comparison between the metabolic activity of the tissue during focal ischemia and global ischemia. Partial global ischemia, which occurs following unilateral carotid occlusion, has little immediate influence on the brain, resulting in differences between both hemispheres only 24 h following the occlusion. In contrast, partial global ischemia due to bilateral carotid occlusion leads to a more severe injury, which is demonstrated by the inability of the brain to cope with metabolic challenges immediately following the occlusion. Partial global ischemia, by unilateral or bilateral carotid occlusion, leads to a more moderate response compared to the core and even the penumbra of focal ischemia. Following the characterization of the metabolic activity in the ischemic tissue, the next step of the study included the evaluation of means to reduce the damage of focal ischemia. Ischemic preconditioning by unilateral and bilateral carotid occlusion did not meet the expectations of treatment to ischemic and reperfusion injury. The results rather show that unilateral or bilateral carotid occlusion prior to MCAO may serve as a model for emboli, in which damage in a main artery leads in a later stage to focal ischemia in a remote area. In contrast, unilateral or bilateral carotid occlusion which was used as ischemic postconditioning proved to be an effective intervention in order to reduce reperfusion injury in focal ischemia. Data obtained in this part of the study may be applicable in dealing with ischemic stroke at the clinic. The MSMP monitoring system, which was used in this study to monitor the function of the mitochondrial and blood supply in various ischemic conditions, has proved to be an effective means for evaluating the ischemic tissue and reveals a novel aspect of ischemic damage. The data collected in the current study may promote the current knowledge regarding the mitochondrial and hemodynamic contribution to the damage occurring due to cerebral ischemia.