The use of intensity-modulated radiation therapy for treatment of dominant intraprostatic lesions may require integration of functional magnetic resonance (MR) imaging with treatment-planning computed tomography (CT). The purpose of this study was to compare prospectively the landmark and iterative closest point methods for registration of CT and MR images of the prostate gland after placement of fiducial markers. The study was approved by the institutional ethics review board, and informed consent was obtained. CT and MR images were registered by using fiducial gold markers that were inserted into the prostate. Two image registration methods--a commonly available landmark method and dedicated iterative closest point method--were compared. Precision was assessed for a data set of 21 patients by using five operators. Precision of the iterative closest point method (1.1 mm) was significantly better (P < .01) than that of the landmark method (2.0 mm). Furthermore, a method is described by which multimodal MR imaging data are reduced into a single interpreted volume that, after registration, can be incorporated into treatment planning.