Successful separations of proteins by capillary electrophoresis in uncoated fused-silica capillaries is limited by adsorption and variable rates of electroendosmosis, which can compromise quantitative accuracy and precision. Operation at extremes of pH to minimize these problems is useful in special cases but is not a general strategy for protein separations. Three alternative strategies are described: use of capillaries coated with a linear hydrophilic polymer, the use of acidic solutions to wash the capillary between runs, and the incorporation of additives into the electrophoresis buffer to minimize adsorption during analysis. Applications of these techniques to protein samples is demonstrated.