An acoustic microfluidic system for miniaturized fluorescence-activated cell sorting (μFACS) is presented. By excitation of a miniaturized piezoelectric transducer at 10 MHz in the microfluidic channel bottom, an acoustic standing wave is formed in the channel. The acoustic radiation force acting on a density interface causes fluidic movement, and the particles or cells on either side of the fluid interface are displaced in a direction perpendicular to the standing wave direction. The small size of the transducer enables individual manipulation of cells passing the transducer surface. At constant transducer activation the system was shown to accomplish up to 700 μm sideways displacement of 10 μm beads in a 1 mm wide channel. This is much larger than if utilizing the acoustic radiation force acting directly on particles, where the limitation in maximum displacement is between a node and an antinode which at 10 MHz is 35 μm. In the automatic sorting setup, the system was demonstrated to successfully sort single cells of E-GFP expressing β-cells.