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We demonstrate a fast miniature microelectro-mechanical-system-based near-infrared fluorescence dual-axis confocal microscope in a 10-mm-diameter package for 3-D imaging in both ex vivo and in vivo samples. The miniature microscope, while in contact with the targeted tissue, can reveal subsurface structure or anatomy as deep as 300 mum. The lateral and axial resolutions are 5 and 7 mum, respectively. Real-time en face mosaicing image of in vivo human skin is demonstrated to enlarge the overall FOV to be over 3 mm at acquisition frame rate of 5 frames/s.