The microheterogeneity of recombinant human erythropoietin (rhEPO) was analyzed by capillary electrophoresis (CE) using a capillary coated with 6,6-ionene. The applicability of a volatile electrolyte for fast analysis of tryptic fragments of rhEPO with online CE-electrospray ionization-mass spectrometry (ESI-MS) was investigated, resulting in a reproducible separation of eleven rhEPO tryptic fragments within 22 min under the following conditions: running buffer 300 mmol/L acetic acid-ammonium acetate (HAc-NH4Ac), pH 4.80, separation voltage -15 kV and capillary temperature 25 degrees C. The proposed method is rapid and effective, and can be used for the structural analysis of related proteins.