Background. Magnetic Resonance Imaging (MRI) is often used in modern day radiotherapy (RT) due to superior soft tissue contrast. However, treatment planning based solely on MRI is restricted due to e. g. the limitations of conducting online patient setup verification using MRI as reference. In this study 3D/3D MRI-Cone Beam CT (CBCT) automatching for online patient setup verification was investigated. Material and methods. Initially, a multi-modality phantom was constructed and used for a quantitative comparison of CT-CBCT and MRI-CBCT automatching. Following the phantom experiment three patients undergoing postoperative radiotherapy for malignant brain tumors received a weekly CBCT. In total 18 scans was matched with both CT and MRI as reference. The CBCT scans were acquired using a Clinac iX 2300 linear accelerator (Varian Medical Systems) with an On-Board Imager (OBI). Results. For the phantom experiment CT-CBCT and MRI-CBCT automatching resulted in similar results. A significant difference was observed only in the longitudinal direction where MRI-CBCT resulted in the best match (mean and standard deviations of 1.85 +/- 2.68 mm for CT and -0.05 +/- 2.55 mm for MRI). For the clinical experiment the absolute difference in couch shift coordinates acquired from MRI-CBCT and CT-CBCT automatching, were