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This manuscript presents high-throughput sorting of cellular-sized microparticles within a three-dimensional microfluidic channel by focused bulk acoustic wave (BAW) produced by a Self-Focusing Acoustic Transducer (SFAT). The focused ultrasound induces a substantially higher acoustic radiation force within the focal region, enabling sorting based on particle size and density. Unlike surface-acoustic-wave-based setups, the BAW-based technique uses a three-dimensional microfluidic channel through which a mixture of particles is transported, while SFAT(s) may be placed at multiple points along the channel for multi-stage sorting. The technique has been successfully used in sorting 50 μm microparticles, which are analogous to cancerous or differentiated Mesenchymal Stem Cells (MSC), from 30 μm microparticles, which are analogous to healthy MSC. The sorting results in 97.5% purity at the smaller microparticle outlet and a 97.2% recovery rate for the smaller particles. The technique allows sorting 650,000 smaller and 142,000 larger microparticles within a mere 10 minutes.