The preparation of cinchonidine (CCND) nanocrystals and their immobilization onto the inner surface of a fused silica capillary was investigated for use in the enantioseparation by capillary electrochromatography. The CCND nanocrystals were prepared by an emulsion method that utilizes crystal growth in an oil-in-water emulsion without a stabilizer. As a result, white-colored aqueous dispersions of organic nanoparticles were obtained. SEM images showed that the prepared CCND nanocrystals were from 300 to 700 nm in size. When the obtained dispersion was introduced into a poly(diallyldimethylammonium chloride) (PDDAC) coated capillary, the nanocrystals were strongly adsorbed onto the inner surface due to an electrostatic interaction between cationic PDDAC and the negatively charged organic nanocrystals. In CCND nanocrystals coated capillary, CEC enantioseparations of racemic amino acids were successfully achieved. The reproducibilities of the detection times were acceptable with a relative standard deviation of less than 7%, indicating that stable nanocrystal coating could be obtained by our proposed method.