Microfluidic fluorescence-activated cell sorters (μFACS) have attracted considerable interest because of their ability to identify and separate cells in inexpensive and biosafe ways. Here a high-performance μFACS is presented by integrating a standing surface acoustic wave (SSAW)-based, 3D cell-focusing unit, an in-plane fluorescent detection unit, and an SSAW-based cell-deflection unit on a single chip. Without using sheath flow or precise flow rate control, the SSAW-based cell-focusing technique can focus cells into a single file at a designated position. The tight focusing of cells enables an in-plane-integrated optical detection system to accurately distinguish individual cells of interest. In the acoustic-based cell-deflection unit, a focused interdigital transducer design is utilized to deflect cells from the focused stream within a minimized area, resulting in a high-throughput sorting ability. Each unit is experimentally characterized, respectively, and the integrated SSAW-based FACS is used to sort mammalian cells (HeLa) at different throughputs. A sorting purity of greater than 90% is achieved at a throughput of 2500 events s . The SSAW-based FACS is efficient, fast, biosafe, biocompatible and has a small footprint, making it a competitive alternative to more expensive, bulkier traditional FACS.