Poly(dimethylsiloxane) (PDMS) is one of the most convenient materials to construct capillary electrophoresis microchips. Even though PDMS has many advantages, its use is often limited by its hydrophobicity. Although it is well-known that the surface properties of PDMS can be modified by anionic surfactants, very little is known regarding the driving forces or the electrophoretic consequences of the adsorption of anionic surfactants. In this work, the adsorption of alkyl surfactants on PDMS was studied by performing electroosmotic flow (microEOF) measurements. In order to mimic the behavior of PDMS microchannels, fused-silica capillaries were coated with PDMS and used for the microEOF measurements. This approach allowed using standard CE instrumentation and provided significant advantages over similar experiments performed on microchips. The change in the microEOF in the presence of surfactants was correlated to the surfactant adsorbed amount which, plotted versus surfactant concentration, gives an adsorption isotherm. The adsorption isotherms were obtained using alkyl surfactants with different chain lengths and head groups. According to our results, the interaction of alkyl surfactants with the PDMS surface is determined by a combination of hydrophobic and electrostatic interactions, where the former is more significant than the latter. The affinity of each surfactant for the PDMS surface was calculated by fitting the adsorption profiles with a Langmuir equation and, in the case of single-charged surfactants, correlated to the corresponding cmc value.