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A nano computed tomography (nano-CT) system has been developed for three-dimensional (3-D) noninvasive biomedical imaging with sub-micrometer resolution. Using modern technologies in x-ray sources, precision mechanics and detection systems, a compact nano-CT scanner has been created for non-invasive imaging of internal microstructure of objects with sub-micrometer resolution. The system allows the imaging of previously unattainable details of internal 3-D micro-architecture in a wide range of applications. The nano-CT scanner consists of a nanofocus x-ray source, a precision object manipulator and high resolution CCD detectors. The source is of the open tube type (transmission) and the minimum focal spot size is < 1um. The object manipulator is composed of three linear motion stages for magnification adjustment(x), alignment(y), positioning(z) and rotating motion stage( ) for sample rotation. The x-ray detector contains a straight fiber-optic coupled CCD. The source-to-detector distance (SDD) is 500 mm and the magnification is from 1.1 to 25 times respectively. All parts of the system operate under computer control from integrated software. In this paper, the reconstructed images using the developed nano CT system for 3-D non-invasive biomedical imaging are presented. The characteristics of nano-CT system are also depicted.