The objective of this study was to assess the utility of CT-MRI image fusion software and compare both prostate volume and localization with CT and MRI studies. We evaluated the differences in clinical volumes in patients undergoing three-dimensional conformal radiation therapy for localized prostate cancer. After several tests performed to ensure the quality of image fusion software, eight patients suffering from prostate adenocarcinoma were submitted to CT and MRI studies in the treatment position within an immobilization device before the start of radiotherapy. The clinical target volume (CTV) (prostate plus seminal vesicles) was delineated on CT and MRI studies and image fusion was obtained from the superimposition of anatomical fiducial markers. A comparison of dose-volume histograms relative to CTV, rectum, bladder and femoral heads was performed for both studies. Image fusion showed a mean overestimation of CTV of 34% with CT compared with MRI. Along the anterior-posterior and superior-inferior direction, CTV was a mean 5 mm larger with CT study compared with MRI. The dose-volume histograms resulting from CT and MRI comparison showed that it is possible to spare a mean 10% of rectal volume and approximately 5% of bladder and femoral heads, respectively. This study confirmed an overestimation of CTV with CT images compared with MRI. Because this finding only allows a minimal sparing of organs at risk, considering the organ motion during each radiotherapy session and the excellent outcomes of prostate cancer treatment with CT based target identification, we are still reluctant to reduce the CTV to that identified by MRI.