The close coupling of neuronal activities to glucose and oxygen metabolism is well established. The imaging of activity-dependent changes in the endogenous fluorescence of NADH and mitochondrial flavoproteins provides the basis for many experimental approaches to visualize brain activities based on local changes in cellular energy metabolism. This chapter summarizes the results of the novel experimental applications of flavoprotein fluorescence for imaging local dynamic coupling of the functional activities of brain cells and temporal linkage to different events (such as electrical activity, calcium flux, and redox changes). These points are discussed in comparison with other methods using endogenous signals (such as deoxygenation of hemoglobin or blood flow changes) and with those using exogenous probes that are sensitive to voltage, calcium, or pH. The technical merits of flavoprotein fluorescence imaging for investigating plastic changes in neural activities and visualizing mouse cortical activities through the intact skull are discussed. Flavoprotein fluorescence imaging is an excellent tool for investigating neural plasticity, and may be a complementary method of functional brain imaging that can be used to understand brain functions.