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Microbubbles (MBs) coated by surfactant or polymer have been shown to be the most effective contrast agents for diagnostic ultrasound contrast imaging and targeted molecular imaging. With the development of both diagnostic and therapeutic applications of ultrasound contrast agents (UCAs), there is a demand for new preparation technologies to provide a high degree of control over MB size, composition, stability and uniformity in response. MBs produced by traditional methods, such as sonication or mechanical agitation, have poor control over MBs' size and uniformity. A polydisperse size distribution may have the inherent limitation of low acoustic backscattering efficiency and uncontrollable safety concern if used in vivo. This study presents successful production of five kinds of monodisperse MBs by flow-focusing method based on four flow-focusing units integrated microfluidic devices. These MBs act as a vehicle to carry fluorescent probe 6-coumarin, tumour-targeted peptide (LyP-1), paclitaxel, superparamagnetic iron oxide Fe3O4 nanoparticles and CdTe/ZnS quantum dots in the lipid shells, respectively. The sizes of MBs are controlled on the order of 2-7 μm by adjusting gas pressure and liquid flow velocity. These functional MBs have the potential applications in emerging areas, such as drug delivery, ultrasound molecular imaging and dual-modality imaging.