Migration behavior of functional polymer particles, such as carboxylic acid- and phenylboric acid-modified polymer particles, was examined in capillary electrophoresis (CE) using migration buffers containing metal ions or saccharides. It was found that the interaction between functional groups on the particles and the specific chemical species in the migration buffers influenced the migration behavior of the polymer particles. The obtained results supported the possibility that CE becomes useful method for examining the property of functional polymer particles.