Integration of functional and structural modalities is essential to functional brain mapping. This paper presents an automatic co-registration system for aligning the coordinate systems between magnetoencephalography/electroencephalo-graphy (MEG/EEG) and magnetic resonance image (MRI) using multiple off-the-shelf RGBD cameras. The system was constructed by using multiple Kinects for Windows V2, which were calibrated for the integration of the captured data of subjects’ heads from multiple views. The integrated point clouds of the head surface captured by Kinects played an intermediate role between MEG/EEG and MRI. MEG/EEG-to-Kinect co-registration was conducted by using 3D locations of three anatomical landmarks, whereas Kinect-to-MRI co-registration was performed by using Gaussian mixture model to align facial part of points automatically segmented from both Kinect data and MRI. Combination of these two co-registration results yields the MEG/EEG-to-MRI transformation. Our evaluation results showed that the proposed system can achieve coordinate system alignment with high accuracy.