We present a novel tracking system for patient head motion inside 3D medical scanners. Currently, the system is targeted at the Siemens High Resolution Research Tomograph (HRRT) PET scanner. Partial face surfaces are reconstructed using a miniaturized structured light system. The reconstructed 3D point clouds are matched to a reference surface using a robust iterative closest point algorithm. A main challenge is the narrow geometry requiring a compact structured light system and an oblique angle of observation. The system is validated using a mannequin head mounted on a rotary stage. We compare the system to a standard optical motion tracker based on a rigid tracking tool. Our system achieves an angular RMSE of 0.11 degrees demonstrating its relevance for motion compensated 3D scan image reconstructions as well as its competitiveness against the standard optical system with an RMSE of 0.08 degrees. Finally, we demonstrate qualitative result on real face motion estimation.