Abstract The face is the preferable biometrics for person recognition or identification applications because person identifying by face is a human connate habit. In contrast to 2D face recognition, 3D face recognition is practically robust to illumination variance, facial cosmetics, and face pose changes. Traditional 3D face recognition methods describe shape variation across the whole face using holistic features. In spite of that, taking into account facial regions, which are unchanged within expressions, can acquire high performance 3D face recognition system. In this research, the recognition analysis is based on defining a set of coherent parts. Those parts can be considered as latent factors in the face shape space. Non-negative matrix Factorisation technique is used to segment the 3D faces to coherent regions. The best recognition performance is achieved when the vertices of 20 face regions are utilised as a feature vector for recognition task. The region-based 3D face recognition approach provides a 96.4% recognition rate in FRGCv2 dataset.