The purpose of this study was to test the superiority of a soft tissue-based setup using cone-beam computed tomography (CBCT) to a bony structure-based setup using the ExacTrac system in intensity-modulated radiotherapy (IMRT) for prostate cancer. We studied 20 patients with localized prostate cancer who received IMRT between November 2010 and February 2012. After the initial setup, the pelvic bony structure-based setup and ExacTrac system were applied. After that, CBCT and a soft tissue-based setup were used. A shift in the isocenter between the ExacTrac-based and CBCT-based setup was recorded in the anterior-posterior (AP), superior-inferior (SI), and left-right (LR) axes. The shift was considered an interfractional prostate shift. Post-treatment CBCT was also taken once a week to measure the intrafractional prostate shift, based on the coordinates of the isocenter between pre- and post-treatment CBCT. The planning target volume (PTV) margins were determined using van Herk's method. We measured the elapsed time required for soft tissue matching and the entire treatment time using CBCT. The means ± standard deviation (SD) of the inter- and intrafractional shifts were 0.9 ± 2.8 mm and -0.3 ± 1.4 mm in the AP, 0.9 ± 2.2 mm and -0.1 ± 1.2 mm in the SI, and 0.1 ± 0.7 mm and -0.1 ± 0.7 mm in the LR directions. The PTV margins in the cases of bony structure-based and soft tissue-based setups were 7.3 mm and 2.7 mm in the AP, 5.8 mm and 2.3 mm in the SI, and 1.9 mm and 1.2 mm in the LR directions. Even though the median elapsed time using CBCT was expanded in 5.9 min, the PTV margins were significantly reduced. We found the calculated PTV margins in the soft tissue-based setup using CBCT were small, and this arrangement was superior to the bony structure-based setup in prostate IMRT.