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Confocal fluorescence endomicroscopy is an emerging endoscopic modality, which allows in vivo microscopic imaging of the mucosal layer of living tissues. In this paper, we will present a low-cost real-time 3D imaging system using an endomicroscope. In the system, the volumetric image data are automatically captured by continuously scanning the surface and subsurface tissue structures without removing tissues from the body or sacrificing animals. Real-time algorithms including feature-based registration of multiple cross-sectional images and GPU-based reconstruction of 3D microstructure as well as instant rendering of the clinical features are developed to allow the clinicians to navigate within the living tissue freely for a much more definitive diagnostic result. The nature of the proposed system enables the clinicians to diagnose various diseases including the early-stage cancers in a non-invasive way. In vivo histology becomes visible and an online diagnosis can potentially be achieved.