We describe a method based on plasma polymerization for the modification and control of the surface properties of poly(dimethylsiloxane) (PDMS) surfaces. By depositing plasma polymerized acrylic acid coatings on PDMS, we succeeded to fabricate stable (several days) hydrophilic and patterned hydrophobic/hydrophilic surfaces. We used this approach to generate direct and (for the first time in this material) double emulsions in PDMS microchannels.