Conventional needle positioning techniques for small animal microinjections are fraught with issues of repeatability and targeting accuracy. To improve the outcomes of these interventions a small animal needle positioning system guided by micro-computed tomography (micro-CT) imaging was developed. A phantom was developed to calibrate the geometric accuracy of micro-CT scanners to a traceable standard of measurement. Use of the phantom ensures the geometric fidelity of micro-CT images for use in image-guided interventions or other demanding quantitative applications. The design of a robot is described which features a remote center of motion architecture and is compact enough to operate within a micro-CT bore. Methods to calibrate the robot and register it to a micro-CT scanner are introduced. The performance of the robot is characterized and a mean targeting accuracy of 149 ± 41 µm estimated. The robot is finally demonstrated by completing an in vivo biomedical application