In this paper we present a method for geometric co-calibration of a single-gantry SPECT-CT small animal imaging system with axially overlapping fields-of-view. Because spatial resolution and noise level differ greatly between both sub-systems the method incorporates different strategies to obtain more accurate calibration values. Firstly, x-ray tomographic calibration is performed on a steel-sphere-phantom which includes 13 steel spheres with 1 mm in diameter, placed on a straight line. Geometric displacement for the high-resolution x-ray CT system (five parameters) is then calculated based on a mathematical analysis of those projection data. Secondly, a 360 degree SPECT-CT imaging of point sources, which are labeled with both radioactivity and x-ray absorber, is applied. With the calculated geometric parameters for the CT system the exact positions of the point sources in the CT volume can be extracted from the CT reconstruction result, and given the positional information in CT as a priori the geometric displacement for the SPECT camera as well as the intrinsic co-alignment between the SPECT and the CT sub-systems (six parameters) is estimated with an iterative optimization strategy (Levenberg-Marquardt). For routine imaging, the calibrated parameters are incorporated into the image reconstruction algorithms applied to the SPECT (MLEM) and CT (FDK) data, respectively, without an additional registration process. Our results show intrinsically aligned images of both modalities with high spatial resolution and low level of mis-alignment. This method is feasible for multi-modality imaging systems with common fields-of-view, however, large difference in spatial resolution and noise level.