Motion-compensated positron emission tomography (PET) has the potential to improve translational investigations by allowing animals to behave normally and respond to external stimuli. Several groups have demonstrated the feasibility of performing motion-compensated brain PET on rodents, obtaining the necessary head motion data using marker-based techniques. However, markerless motion tracking would simplify animal experiments, be less invasive, and potentially provide more accurate pose estimates over a greater range of motion. We describe a markerless stereo motion tracking system and demonstrate the feasibility of using this system to obtain highly accurate (< 0.2 mm) pose estimates for realistic motion of a taxidermied rat head. The system is based on the simultaneous localization and mapping (SLAM) framework used in mobile robotics and involves building a consistent set of landmarks on the head for pose estimation. Pose measurements using the markerless system were approximately 10 times more accurate than a state-of-the-art marker-based system. Planning of experiments to validate markerless tracking in microPET imaging of awake animals is currently underway.