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Dosimetric implications of two registration based patient positioning methods in prostate image guided radiation therapy (IGRT) Background. We compare the dosimetry of daily patient positioning based on prostate matching versus bone matching for patients treated with helical tomotherapy. Methods. Ninety-nine pre-treatment 3D megavoltage (MV) CT images of four high risk prostate patients were registered to their respective planning images using two automatic registration algorithms, one achieving bone matching and the other prostate matching. Dose distributions that would have been delivered had patient positioning been based on each matching method were evaluated. Contours were delineated on each MVCT image and prostate, bladder, and rectum dose volume histograms were compared for each image guidance strategy using endpoints adapted from inverse planning constraints. Results. The standard deviation of per fraction prostate ΔD95 values, defined as prostate matching D95 minus bone matching D95, was 0.01 Gy (Range: -0.02 to 0.02 Gy). Defined analogously, bladder ΔD45 and rectum ΔD30 values were 0.12 Gy (Range: -0.22 to 0.52 Gy) and 0.14 Gy (Range: -0.40 to 0.34 Gy), respectively. Conclusions. Bladder ΔD45 and rectum ΔD30 standard deviation values corresponding to 6.1% and 7.5% of their respective planning constraints suggesting critical structure doses are dependent on positioning method. A relationship between critical structure dosimetry and the direction of daily prostate motion was also observed.