The human face is one of the most important biometric modalities for automatic authentication. Three-dimensional face recognition exploits facial surface information. In comparison to illumination based 2D face recognition, it has good robustness and high fake resistance, so that it can be used in high security areas. Nevertheless, as in other common biometric systems, potential risks of identity theft, cross matching and exposure of privacy information threaten the security of the authentication system as well as the user’s privacy. As a crucial supplementary of biometrics, the template protection technique can prevent security leakages and protect privacy. In this chapter, we show security leakages in common biometric systems and give a detailed introduction on template protection techniques. Then the latest results of template protection techniques in 3D face recognition systems are presented. The recognition performances as well as the security gains are analyzed.