Sodium dodecyl sulfate-capillary gel electrophoresis (SDS-CGE) and capillary isoelectric focusing (CIEF) were employed to characterize and compare ricin E purified from the small grain seeds of Ricinus communis with ricin D isoform. During the purification of ricin E using ion-exchange and size-exclusion chromatography, SDS-CGE was found to be useful for monitoring the efficiencies of purification steps. SDS-CGE showed that the molecular size of ricin E was not significantly different from that of ricin D, which was confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. CIEF was useful for discriminating ricin E from ricin D based on their isoelectric points (pI). The pI values of ricin E and D were 8.6-8.8 and 7.0-7.4, respectively. This study demonstrates the usefulness of SDS-CGE and CIEF for the characterization of ricin toxins.