Micro Computed Tomography (micro-CT) was suggested in biomedical research to investigate tissues and small animals. Its use to characterize bone structures, vessels (e.g. tumor vascularization), tumors and soft tissues such as lung parenchyma has been shown. When co-registered, micro-CT can add structural information to other small animal imaging modalities. However, due to fundamental CT principles, high-resolution imaging with micro-CT demands for high x-ray doses and long scan times to generate a sufficiently high signal-to-noise ratio. Long scan times in turn make the use of extravascular contrast agents difficult. Recently introduced flat-panel based mini-CT systems offer a valuable tradeoff between resolution (∼200 μm), scan time (0.5 s), applied x-ray dose and scan field-of-view. This allows for angiography scans and follow-up examinations using iodinated contrast agents having a similar performance compared to patient scans. Furthermore, dynamic examinations such as perfusion studies as well as retrospective motion gating are currently implemented using flat-panel CT. This review summarizes applications of experimental CT in basic research and provides an overview of current hardware developments making CT a powerful tool to study tissue morphology and function in small laboratory animals such as rodents.