Microfluidic systems have faced challenges in handling real samples and the chip interconnection to other instruments. Here we present a simple interface, where surface acoustic waves (SAWs) from a piezoelectric device are coupled into a disposable acoustically responsive microfluidic chip. By manipulating droplets, SAW technologies have already shown their potential in microfluidics, but it has been limited by the need to rely upon mixed signal generation at multiple interdigitated electrode transducers (IDTs) and the problematic resulting reflections, to allow complex fluid operations. Here, a silicon chip was patterned with phononic structures, engineering the acoustic field by using a full band-gap. It was simply coupled to a piezoelectric LiNbO3 wafer, propagating the SAW, via a thin film of water. Contrary to the use of unstructured superstrates, phononic metamaterials allowed precise spatial control of the acoustic energy and hence its interaction with the liquids placed on the surface of the chip, as demonstrated by simulations. We further show that the acoustic frequency influences the interaction between the SAW and the phononic lattice, providing a route to programme complex fluidic manipulation onto the disposable chip. The centrifugation of cells from a blood sample is presented as a more practical demonstration of the potential of phononic crystals to realize diagnostic systems.© (2011) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.