This technical note reports on a new procedure to on-column-label organelles sampled from a tissue cross section into a fused silica capillary. These organelles are then analyzed by capillary electrophoresis with postcolumn laser-induced fluorescence detection. In this procedure, the fluorescent label does not come in contact with the tissue, which facilitates visualization of the sampled tissue cross section. In addition, on-column labeling allows for better control of the reaction time and fluorescent label concentrations. As a proof-of-principle, we show results of mitochondria from rat gastrocnemius muscle cross sections that were on-column-labeled with 10-N-nonyl acridine orange (NAO), a mitochondrion-specific probe, and compare them with results for NAO in-tissue labeling of the same tissue. The new organelle labeling procedure reported here may easily be extended to the analysis of individual organelles in other biological samples and may become a valuable tool in studies investigating the role of mitochondria in muscle aging and exercise physiology.