The rapid proliferation of micro-computed tomography (micro-CT) scanners in preclinical small animal studies has created a need for a method on scanner performance evaluation and scan parameter optimisation. The purpose of this study was to investigate the performance of the scanner with a dedicated micro-CT phantom. The phantom was developed with different independent sections that allow for measurement of major scanner characteristics such as uniformity, linearity, contrast response, dosimetry and resolution. The results of a thorough investigation are discussed.