Polyethylene oxide-mediated capillary sodium dodecyl sulfate-electrophoresis is a recently established, high-resolution separation method for fast purity check and molecular mass assessment of protein molecules. The effects of the sieving polymer chain length and concentration on the separation mechanism of sodium dodecyl sulfate-protein complexes were examined. The studies aimed to clarify whether the separation can be described by either the Ogston sieving theory, or the reptation or reptation-with-stretching theory. Polyethylene oxides with molecular masses of 100,000, 300,000 and 900,000 Da were used as separation matrices at various concentrations ranging from 1-4%, 0.5-2% and 0.25-1%, respectively. The separation phenomena was examined using a standard protein test mixture containing six proteins in the molecular mass range of 14,200-97,400 Da. A possible separation mechanism of reptation with stretching is suggested, where separation performance was improved with increasing sieving polymer chain lengths and/or concentration.