In this study a capillary electrophoresis (CE) application technique uses different buffers in the equilibration process (equilibrating buffer) and the electrophoresis process (working buffer) is developed. When low concentration phosphate buffer is used to equilibrate and high concentration buffer as working buffer, the sample is stacked effectively. Contrarily the separation of samples bovine serum albumin (BSA) is enhanced when high concentration phosphate buffer is used as the equilibrating buffer. The addition of methanol in the working buffer effectively improves the separation of BSA.