Summary: Positron emission tomography (PET) is an important tool in preclinical studies to measure the metabolism of small animals. However, anesthetics have to be applied ti so that animals lie motion-free in the scanner during the time of the PET scan. Since anesthetics influence the metabolism, the resulting measurements are necessarily biased. Therefore, a method to measure awake animals inside a PET scanner is desirable and would broaden the possibilities for functional imaging in preclinical studies. In this work a tracking system based on optical cameras is presented that allows to track the head pose of a mouse or a rat during a PET scan while the animal is roaming freely inside a cage within the field of view of the scanner. Using the extracted motion information, it is possible to correct the acquired PET data for motion and to reconstruct sharp PET images. This work describes the developed hardware and the applied tracking algorithm in detail. Quantitative validations for all components of the tracking system have been performed and the developed tracking algorithm was validated extensively based on five animal experiments. At the end of this work, motion-corrected PET reconstructions of the performed experiments with freely-moving mice during a PET scan are presented as a proof of concept.