Microspectrofluorometric methods were developed for detection of mitochondrial metabolites and marker molecules in living cells. After excitation in the near UV and blue spectral ranges, respiratory-deficient strains of Saccharomyces cerevisiae showed higher levels of intrinsic fluorescence than corresponding wild types. This may be attributed to an increased emission by NADH and flavin molecules of the mutants. After incubation with the mitochondrial marker rhodamine 123, there was a strong indication that an energy transfer from flavin to rhodamine molecules occurred, which was more pronounced for the respiratory-deficient yeast strains. Skin fibroblasts obtained from patients with mitochondrial diseases showed approximately the same levels of autofluorescence and energy transfer but higher variances than a control cell line. These higher variances may result from a coexistence of intact and defective mitochondria.