A capillary chromatography system was developed using an open capillary tube and a water-acetonitrile (hydrophilic)-ethyl acetate (hydrophobic) mixture carrier solution. In this study, we examined the effects of the inner-wall characteristics of a fused-silica capillary tube on the separation performance in this system. Untreated (silanol group-intact) and inactivated (silanol group-end-blocked) fused-silica capillary tubes were used. The mixture analyte of 1-naphthol and 2,6-naphthalenedisulfonic acid was injected into two types of capillary tubes. They were eluted from both tubes in this order with water-acetonitrile-ethyl acetate (volume ratio 2:7:4) mixture carrier solution, and eluted in reverse order with water-acetonitrile-ethyl acetate (volume ratio 15:3:2). The peak shapes observed here were analyzed while considering the inner-wall characteristics of the capillary tubes from the viewpoint of the tube radial distribution of the carrier solvents in the tubes.