Background: For the purpose of individual clinical target volume assessment in radiotherapy of prostate cancer, MRSI was used as a molecular imaging modality with MRI and CT images. Materials and Methods: The images of 20 prostate cancer patients were used in this study. The MR and MRSI images were registered with CT ones using non-rigid registration technique. The CT based planning (BP), CT/MRI BP and CT/MRSI BP was performed for each patient. For plan evaluation, Dose Volume Histograms (DVHs) data were used. A paired sample T-test was used for the analysis of the obtained data. Results: The percentage of variation of CTVMRI to CTVCT and PTVMRI to PTVCT were 12.83% and 8.97%, respectively. CTVMRSI and PTVMRSI were 21% and 27.41% more than their corresponding values of CT volumes. The mean percentage of variation in rectum volume that received 60% of the prescribe dose (V60R) in MRSI/CT BP relative to CT BP was 14.66%. Conclusion: The use of MRSI in detecting of prostate adenocarcinoma could provide some decisive information to determine optimum volume and safe margin for target definition to improve adaptive radiotherapy in prostate cancer.