In radiotherapy, target tissues are defined best on MR images due to their superior soft tissue contrast. Computed tomography imaging is geometrically accurate and it is needed for dose calculation and generation of reference images for treatment localization. Co-registration errors between MR and computed tomography images can be eliminated using magnetic resonance imaging-only based treatment planning. Use of ionizing radiation can be avoided which is especially important in adaptive treatments requiring several re-scans. We commissioned magnetic resonance imaging-only based procedure for external radiotherapy, treatment planning of the prostate cancer. Geometrical issues relevant in radiotherapy, were investigated including quality assurance testing of the scanner, evaluation of the displacement of skin contour and radiosensitive rectum wall, and detection of intraprostatic fiducial gold seed markers used for treatment localization. Quantitative analysis was carried out for 30 randomly chosen patients. Systematic geometrical errors were within 2.2 mm. The gold seed markers were correctly identified for 29 out of the 30 patients. Positions of the seed midpoints were consistent within 1.3 mm in magnetic resonance imaging and computed tomography. Positional error of rectal anterior wall due to susceptibility effect was minimal. Geometrical accuracy of the investigated equipment and procedure was sufficient for magnetic resonance imaging-only based radiotherapy, treatment planning of the prostate cancer including treatment virtual simulation. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.