Migration-time reproducibility is essential in the use of capillary electrophoresis to identify components in mixtures. Two methods based on the migration time of either one or two reference markers are proposed for improving migration time reproducibility. These methods were evaluated to determine the migration time reproducibility for phenylthiohydantoin-amino acids, fluorescein thiohydantoin-amino acids, and tetramethylrhodamine labeled oligosaccharides. In the best case, the relative standard deviation of the migration time was reduced from >3% without correction to <0.04% with the two-marker correction.