Middle cerebral artery occlusion (MCAO), which leads to focal cerebral ischemia, serves as an experimental model for brain stroke. There is a large variation in protocols and techniques using the MCAO model, which may affect the outcomes seen in different studies. The current work presents and compares the diverse responses in mitochondrial NADH and cerebral blood flow (CBF) following focal ischemia induced by the MCAO technique. Ninety-six Wistar rats underwent focal cerebral ischemia by MCAO, and monitored in the core and the penumbra using a unique Multi-Site-Multi-Parametric (MSMP) system, which measures mitochondrial NADH using the fluorometric technique, and CBF using laser Doppler flowmetry (LDF). Following MCAO, 58% of the experiments yielded expected responses, namely a decrease in CBF and an increase in NADH. However, 42% of the experiments showed six other profiles of responses, in which CBF, NADH and tissue reflectance (Ref) responded differently. These profiles included: ischemia without reperfusion, death following reperfusion, minor responses in parameters during ischemia, CBF elevation in the penumbra following MCAO, spontaneous early reperfusion and late reperfusion. These results demonstrate that MCAO is a complex model, which may lead to different responses other than the common expected outcomes, i.e. mitochondrial damage and reduced blood flow in both core and penumbra. The MSMP monitoring system may serve as an important tool in early diagnosis of successful focal cerebral ischemia, reducing the percentage of unsuccessful experiments.