This chapter introduces the concept of using ultrasound for the manipulation of small particles in fluids for in vitro systems, and in particular how this can be applied to bacterial cells in suspension. The physical phenomena that lead to this effect are discussed, including radiation forces, cavitation, and streaming, thus allowing an appreciation of the limitations and applicability of the technique. Methods for generating ultrasound are described, together with practical examples of how to construct manipulation systems, and detailed examples are given of the current practical techniques of particle manipulation. These include filtration of particles for both batch and continuous systems, concentration of particles, cell washing from one fluid into another, fractionation of cellular populations, and trapping of material against flow. Concluding remarks discuss potential future applications of ultrasonic technology in microfluidic bacterial analysis and predict that it will be a significant tool in cell sample processing, with significant integration potential for Lab-On-Chip technologies