Abnormal mitochondrial function was reported in patients and models for amyotrophic lateral sclerosis (ALS). It is therefore important to set up sensitive tools for the monitoring of active agents that enhance energy metabolism delay onset, and extend lifespan of transgenic G93A-SOD1 ALS mice. In this report, primary motor cortex slices from G93A mice at different stages of disease were studied, using NAD(P)H autofluorescence post-synaptic signals following ultraviolet stimuli, as a probe to evaluate mitochondrial function. We observed consistent age-related alterations of responses in G93A primary motor cortex slices versus controls. We conclude that NAD(P)H autofluorescence post-synaptic signal is a highly sensitive real-time technique to detect mitochondrial function failure in primary cortex from living tissues.