We examined the elution behavior of isoluminol isothiocyanate (ILITC)-labeled proteins (alcohol dehydrogenase (ADH) and bovine serum albumin (BSA)) in a capillary chromatography system using an untreated fused-silica capillary tube and a water acetonitrile ethyl acetate mixture carrier solution. The mixture of ILITC and ILITC-labeled protein (ADH or BSA) was analyzed using this system with a chemiluminescence detector; the ILITC and the labeled protein were separated in this order with an organic solvent-rich carrier solution, while they were eluted in the reverse order with a water-rich carrier solution. In addition, the mixture of ILITC, ILITC-labeled ADH, and ILITC-labeled BSA was added to this system, and the analytes of the mixture were separated and confirmed with the individual peaks on the chromatograms.