Here we report on the analysis of mitochondrial preparations by capillary electrophoresis with postcolumn laser-induced fluorescence detection. Individual mitochondria are detected by fluorescent labeling with the mitochondrion-selective probe, 10-nonyl acridine orange. Interactions between the organelles and the capillary walls are controlled by derivatization of the capillaries with poly(acryloylaminopropanol). As expected from the presence of charged groups in their outer membranes, isolated mitochondria have intrinsic electrophoretic mobilities. This property may be influenced by variations in size, morphology, membrane composition, and damage caused during the isolation procedure. The mobility distributions of mitochondria isolated from NS1 and CHO cells ranged from -1.2 × 10-4 to -4.3 × 10-4 cm2V-1 s-1 and -0.8 × 10-4 to -4.2 × 10-4 cm2 V-1 s-1, respectively. Furthermore, there seems to be no correlation between the density of the mitochondrial fraction and the resultant electrophoretic mobility distribution. These results suggest a new method for characterization of organelle fractions and for counting individual organelles.