The aim of the study was to compare clinical target volumes defined by CT and MRI for 3 dimensional conformal external beam radiotherapy of prostate cancer. CT and T2-weighed MRI images with 3 mm slice thickness were acquired for 13 patients with clinically organ-confined prostate cancer. Target volumes were contoured by two clinicians ("AP" and "SZ") experienced in prostate radiotherapy. Two clinical target volumes were defined: prostate (CTVpros) and prostate with a margin including the proximal 1 cm of the seminal vesicles (CTVpvs). Eight clinical target volumes were outlined for all patients: CTVprosAPCT, CTVprosAPMR, CTVpvsAPCT, CTVpvsAPMR, CTVprosSZCT, CTVprosSZMR, CTVpvsSZCT, CTVpvsSZMR. Volumes were measured in cm3. The volumes of different PTVs were compared using the Student's t-test. Mean CTVpros and CTVpvs using CT vs. MRI were 36.9 (range:13.8-121) vs. 32.0 (9.7-120.1) (p=0.0002), and 77.2 (30.5-209.5) vs. 67.6 (29.8-191.1) (p=0.0001), respectively. Mean CTVprosAPCT vs. CTVprosAPMR were 39.2 vs. 32.0 (p<0.00005), respectively. Mean CTVprosSZCT vs. CTVprosSZMR were 34.6 vs. 31.9 (p=0.15). Mean CTVpvsAPCT vs. CTVpvsAPMR were 85.8 vs. 70.9 (p<0.00006). Mean CTVpvsSZCT vs. CTVpvsSZMR were 68.6 vs. 64.4 (p=0.14). Interobserver difference for CTVpros defined by CT images was significant (39.2 vs. 34.6; p=0,0058). However, the difference was not significant using MRI images (32.0 vs. 31.9; p=0.93). Interobserver differences for CTVpvs were significant using either CT (85.8 vs. 68.6; p=0.0001) or MRI (70.9 vs. 64.4; p=0.004). Ratio of mean volumes contoured by the two observers were 1,12 (CT) vs. 1 (MRI) for CTVpros and 1,2 (CT) vs. 1,09 (MRI) for CTVpvs. Clinical target volumes defined for prostate cancer external beam radiotherapy by MRI images are significantly smaller compared to CT image based contouring. The magnitudes of differences are observer dependent. The use of MRI decreases the interobserver difference of mean volumes with 11% and 12% for CTVpvs and CTVpros.