A 50 μm capillary that has been etched with ammonium hydrogen difluoride is evaluated as a separation medium for capillary electrochromatography. For a tryptic digest of transferrin, the etched capillary gave better resolution (more peaks in the overall peptide map) and longer retention than separations done under identical experimental conditions on an unetched fused-silica capillary. Resolution on the etched capillary was improved by lowering the voltage from 300 to 267 V/cm. A four-component protein sample also resulted in longer retention on an echted capillary than on an unetched fused-silica capillary that were both coated with Polybrene. After correction for differences in electroosmotic flow between the two capillaries, the calculated electrophoretic mobilities for all four proteins were lower on the etched capillary than on the unetched fused-silica capillary. The results of both the tryptic digest and protein experiments strongly indicate the presence of chromatographic effects on the etched capillary that contribute to the increased retention and improved resolution with respect to the unetched fused-silica capillary.