Small animal imaging has recently become an area of increased interest because more human diseases can be modeled in transgenic and knockout rodents. Current micro-CT systems are capable of achieving spatial resolution on the order of 10 μm, giving highly detailed anatomical information. However, the speed of data acquisition of these systems is relatively slow, when compared with clinical CT systems. Dynamic CT perfusion imaging has proven to be a powerful tool clinically in detecting and diagnosing cancer, stroke, pulmonary and ischemic heart diseases. In order to perform this technique in mice and rats, quantitative CT images must be acquired at a rate of at least 1 Hz. Recently, a research pre-clinical CT scanner (eXplore Ultra, GE Healthcare) has been designed specifically for dynamic perfusion imaging in small animals. Using an amorphous silicon flat-panel detector and a clinical slip-ring gantry, this system is capable of acquiring volumetric image data at a rate of 1 Hz, with in-plane resolution of 150 μm, while covering the entire thoracic region of a mouse or whole organs of a rat. The purpose of this study was to evaluate the principal imaging performance of the micro-CT system, in terms of spatial resolution, image uniformity, linearity, dose and voxel noise for the feasibility of imaging mice and rats. Our investigations show that 3D images can be obtained with a limiting spatial resolution of 2.7 line pairs per mm and noise of 42 HU, using an acquisition interval of 8 seconds at an entrance dose of 6.4 cGy.