The cationic dye capillary electrophoresis method successfully differentiated 10 blue ballpoint pen inks that were extracted from mock forensic samples. Identification of five components (dyes and additives) was sufficient to distinguish the inks. Direct infusion electrospray ionization mass spectrometry was used to confirm the assignment of capillary electrophoresis peaks. The use of capillary electrophoresis for ballpoint pen ink analysis addresses many of the disadvantages of thin-layer chromatography of ink extracts. Thin-layer chromatography is not typically automated; thus, the spotting of a slide and the measuring of retardation factor values are difficult to reproduce. In addition, spectroscopic data are not obtained, although densitometry can be used to analyze spots for quantitative data when compared to a standard. This assumes that the chemical identity is known. Often the spots are faint, making them difficult to see. If an ink sample is composed of two or more similar dyes, then thin-layer chromatography can result in two or more unresolved spots with nearly identical colors. This scenario requires multiple runs with different solvent systems, which is time-consuming. Capillary electrophoresis, on the other hand, is completely automated, and method development is rapid. A photodiode array detector can be used to obtain ultraviolet-visible spectra of each component. Data are stored electronically, allowing the development of an automated, searchable library of electropherograms and ultraviolet-visible spectra, while eliminating the need for an environmentally controlled storage space. 16 references