Heparin is widely used as an anticoagulant for the treatment and prevention of thrombotic disorders. Recently, hundreds of cases of anaphylactic reaction as adverse effects were reported by the presence of contaminating oversulfated chondroitin sulfate (OSCS) in some heparin preparations. In addition, these heparin preparations often contaminated dermatan sulfate (DS). Unfortunately, the Japanese Pharmacopoeia (JP) does not include appropriate purity tests. In the present paper, we show that capillary electrophoresis (CE) is a powerful tool for the analysis of OSCS and DS in heparin preparations. CE method shows high resolution and good quantification of OSCS in heparin preparations. This method (OSCS method) was evaluated for accuracy (93.7 %), repeatability (R.S.D.=2.11), linearity (R²=0.9996), detection limit (0.1% OSCS) and specificity. In contrast, DS was not able to be detected in high sensitivity by OSCS method. However, a modified CE method (DS method) using the buffer at lower pHs showed good parameters for accuracy (88.1%), repeatability (R.S.D.=1.99), linearity (R²=0.9998), detection limit (0.25% DS) and specificity. In conclusion, CE will be an alternative to the NMR method which is being adopted for purification test of heparin sodium in the present version of JP.