Several factors during the scanning process, image reconstruction and geometry of an imaging system, influence the spatial resolution of a computed tomography imaging system. In this work, the spatial resolution of a state of the art flat panel detector-based cone beam computed tomography breast imaging system is evaluated. First, scattering, exposure level, voltage, voxel size, pixel size, back-projection filter, reconstruction algorithm, and number of projections are varied to evaluate their effect on spatial resolution. Second, its uniformity throughout the whole field of view is evaluated as a function of radius along the x-y plane and as a function of z at the center of rotation. The results of the study suggest that the modulation transfer function is mainly influenced by the pixel, back-projection filter, and number of projections used. The evaluation of spatial resolution throughout the field of view also suggests that this imaging system does have a 3-D quasi-isotropic spatial resolution in a cylindrical region of radius equal to 40 mm centered at the axis of rotation. Overall, this study provides a useful tool to determine the optimal parameters for the best possible use of this cone beam computed tomography breast imaging system.