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Small-animal imaging technology has been rapidly developed for longitudinal screening of laboratory animals raised with disease developments or genetic manipulations. Micro-CT is a noninvasive imaging modality used to assess morphology and function in small-animal imaging. Geometric calibration involves the estimation of a set of parameters that describes the geometry of such systems, and is essential for accurate image reconstruction. Noo F et al (2000) have proposed a new analytic method for calibration of x-ray cone-beam scanners that use a circular path for the cone vertex. In this paper, we use this analytic calibration method for the estimation of the geometric parameters of a practical small-animal imaging micro-CT system. We improve calibration phantom of this method in order to make it more suitable for micro-CT system. The overall performance of the micro-CT system is demonstrated in some results of small-animal imaging. The projection images demonstrated that the adopt method is robust and easy to implement with high precision.