Anionic, water-soluble siloxane polymers modified with different lengths of alkyl chains have very different selectivity than sodium dodecyl sulfate (SDS) micelles when used as pseudostationary phases in electrokinetic chromatography. The siloxanes in this study are random copolymers with side chains bearing sulfonate groups and alkyl groups (C-8, C-12, or C-18), with the proportion of alkyl groups between 10 and 25% of the total. The differences in selectivity have been studied by linear solvation energy relationships (LSERs). The siloxanes in general have been found to be more cohesive, less polar, more able to interact with solutes through n- and pi -electrons, and more able to accept hydrogen bonds than SIDS micelles, while the ability to act as hydrogen bond donors is not significantly different than SIDS micelles. In addition, the performance in a pH 7.0 Tris buffer has been investigated and the siloxanes were found to have higher methylene selectivities and more variable electrophoretic mobilities than in borate buffers.