Novalis Tx ExacTrac X‐ray system has the 6D adjustment ability for patient setup. Limited studies exist about the setup uncertainty with ExacTrac X‐ray system for IMRT prostate treatment with fiducial markers implanted. The purpose of this study is to investigate the marker‐based prostate IMRT treatment setup uncertainty using ExacTrac 6D IGRT ability for patient setup. Forty‐three patients with prostate cancers and markers implanted have been treated on the Novalis Tx machine. The ExacTrac X‐ray system has been used for the patient pretreatment setup and intratreatment verification. In total, the shifts data for 1261 fractions and 3504 correction times (the numbers of X‐ray images were taken from tube 1 and tube 2) have been analyzed. The setup uncertainty has been separated into uncertainties in 6D. Marker matching uncertainty was also analyzed. Correction frequency probability density function was plotted, and the radiation dose for imaging was calculated. The minimum, average, and maximum translation shifts were: −5.12±3.89 mm, 0.20±2.21 mm, and 6.07±4.44 mm, respectively, in the lateral direction; −6.80±3.21 mm, −1.09±2.21 mm, and 3.12±2.62 mm, respectively, in the longitudinal direction; and −7.33±3.46 mm, −0.93±2.70 mm, and 5.93±4.85 mm, respectively, in the vertical direction. The minimum, average, and maximum rotation shifts were: −1.23° ± 1.95°, −0.25° ± 1.30°, and −2.38° ± 2.91°, respectively, along lateral direction; −0.67° ± 0.91°, −0.10° ± 0.61°, and −1.51° ± 2.04°, respectively, along longitudinal direction; and −0.75° ± 1.01°, −0.02° ± 0.50°, and −0.82° ± 1.13°, respectively, along vertical direction. On average, each patient had three correction times during one fraction treatment. The radiation dose is about 3 mSv per fraction. With the ExacTrac 6D X‐ray system, the prostate IMRT treatment with marker implanted can achieve less than 2 mm setup uncertainty in translations, and less than 0.25° in rotations as overall interfraction mean error. The imaging dose is less than kV (CBCT) for setup verification.PACS number: 87.55.km, 87.55.Qr, 87.56.bd