This paper describes an acoustic method for inducing rotating vortex flows in microchannels. An ultrasonic crystal is used to create an acoustic standing wave field in the channel and thus induce a Rayleigh flow transverse to the laminar flow in the channel. Mixing in microchannels is strictly diffusion-limited because of the laminar flow, a transverse flow will greatly enhance mixing of the reactants. This is especially evident in chemical microsystems in which the chemical reaction is performed on a solid phase and only one reactant is actually diffusing. The method has been evaluated on two different systems, a mixing channel with two parallel flows and a porous silicon micro enzyme reactor for protein digestion. In both systems a significant increase of the mixing ratio is detected in a narrow band of frequency for the actuating ultrasound.