Microscopic energy transfer spectroscopy was established using mixed solutions of reduced nicotinamide adenine dinucleotide (NADH) and the mitochondrial marker rhodamine 123 (R123). This method was applied to probe mitochondrial malfunction of cultivated endothelial cells from calf aorta incubated with various inhibitors of specific enzyme complexes of the respiratory chain. Autofluorescence of the coenzyme NADH as well as energy transfer efficacy from excited NADH molecules (energy donor) to R123 (energy acceptor) were measured by time-gated fluorescence spectroscopy. Because intermolecular distances in the nanometer range are required for radiationless energy transfer, this method is suitable to probe selectively mitochondrial NADH. Autofluorescence of endothelial cells usually exhibited a weak increase after specific inhibition of enzyme complexes of the respiratory chain. In contrast, pronounced and statistically significant changes of energy transfer efficacy were observed after inhibition of the same enzyme complexes. Detection of NADH and R123 in different nanosecond time gates following the exciting laser pulses enhances the selectivity and improves quantification of fluorescence measurements. Therefore, time-gated energy transfer spectroscopy is suggested to be an appropriate tool for probing mitochondrial malfunction.