Imaging conscious animals in small animal positron emission tomography (PET) presents a significant challenge, and some form of motion compensation will normally be necessary. In this work, a commercial optical motion tracker called the Micron Tracker has been adapted to the microPET system for this purpose. We evaluated marker size limits, performed a spatial calibration for the devices, developed a synchronization method, and carried out a phantom study involving multiple, discrete 3D movements to test key components of the motion tracking system. We have demonstrated that small and lightweight markers (approx. 15mm x 18mm) are feasible with this system for 3D motion tracking, Calibration accuracy was 0.46mm RMS.Synchronization of the data streams was achieved with a precision of approximately 20ms. Moreover, a marked reduction in motion artifacts was demonstrated in the phantom study. The techniques and results presented here demonstrate the feasibility of adapting the Micron Tracker to the microPET environment for motion tracking of small laboratory animals. There is scope to improve on limitations in synchronization and further optimize marker design to achieve better pose accuracy and precision.