Micro-CT scanners are becoming widely used for in-vivo imaging of small laboratory animals. However, imaging of chest area remains a challenging task due to periodic respiratory and cardiac motion. To reduce motion artifacts and to allow dynamic imaging, we propose a retrospective synchronization method for scans of chest area in in-vivo micro-CT scanners. In this synchronization method, we acquire projection images in a step-and-shoot mode, where multiple images are acquired covering more than one motion cycle at each step with exact time marks of every acquisition. In the meanwhile motion signals are recorded. An offline sorting program sorts images into corresponding motion phases. Compared to other methods, our method has several advantages: 1. flexible in sorting; 2. maximum utilization of radiation dose applied to the animal; 3. possibility for 4D dynamic imaging; 4. can be used during irregular breathing cycle. Initial results indicate that the proposed method is adequate.