Autofluorescence has been used as an indirect measure of neuronal activity in isolated cell cultures and brain slices, but only to a limited extent in vivo. Intrinsic fluorescence signals reflect the coupling between neuronal activity and mitochondrial metabolism, and are caused by the oxidation/reduction of flavoproteins or nicotinamide adenine dinucleotide (NADH). The present study evaluated the existence and properties of these autofluorescence signals in the cerebellar cortex of the ketamine/xylazine anesthetized mouse in vivo. Surface stimulation of the unstained cerebellar cortex evoked a narrow, transverse beam of optical activity consisting of a large amplitude, short latency increase in fluorescence followed by a longer duration decrease. The optimal wavelengths for this autofluorescence signal were 420-490 nm for excitation and 515-570 nm for emission, consistent with a flavoprotein origin. The amplitude of the optical signal was linearly related to stimulation amplitude and frequency, and its duration was linearly related to the duration of stimulation. Blocking synaptic transmission demonstrated that a majority of the autofluorescence signal is attributed to activating the postsynaptic targets of the parallel fibers. Hypothesized to be the result of oxidation and subsequent reduction of flavoproteins, blocking mitochondrial respiration with sodium cyanide or inactivation of flavoproteins with diphenyleneiodonium substantially reduced the optical signal. This reduction in the autofluorescence signal was accomplished without altering the presynaptic and postsynaptic components of the electrophysiological response. Results from reflectance imaging and blocking nitric oxide synthase demonstrated that the epifluorescence signal is not the result of changes in hemoglobin oxygenation or blood flow. This flavoprotein autofluorescence signal thus provides a powerful tool to monitor neuronal activity in vivo and its relationship to mitochondrial metabolism.