Mitochondrial dysfunction and degeneration are associated with neurodegenerative disorders. A dysfunctional mitochondrial electron transport chain (ETC) impairs ATP production and accelerates the generation of free radicals. To quantify ETC activity, solution-spectrophotometric assays and histochemical reactions on blue native polyacrylamide gel electrophoresis (BN-PAGE) gels have been used. These methods, however, do not provide information regarding mitochondrial ETC activities associated with specific regions in the central nervous system (CNS). Because neurodegenerative diseases often strike a specific subset of neurons within specific regions in the CNS, reliable methods for quantifying mitochondrial ETC activities in selected CNS regions are needed. We have studied the quantitative range of in situ histochemical assays for ETC complex I, II and IV and determined the optimal conditions for quantification of these ETC complex activities. We also demonstrate that these assays can detect a decrease in mitochondrial ETC activities in the ventral horn of spinal cords isolated from a transgenic mouse model for amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease.