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The aim is to compute all sources of geometrical uncertainty in prostate radiotherapy using fiducial markers and determine the safety treatment margins. Based on the markers position, correlations between prostate rotation/deformation and rectal and bladder fillings as well as changes in prostate volume during the treatment course are analyzed. The study includes 375 pre-treatment CBCT images from 15 prostate cancer patients treated with hypofractionated radiotherapy. The position coordinates of the markers were obtained from each image acquisition. In addition, rectum and bladder were outlined on CBCTs. The intrafractional error was estimated by an additional post-treatment CBCT acquired on alternate days. Tau-Kendall analysis was performed to correlate organ fillings with prostate rotation/deformation. Delineation uncertainty was assessed from contours of 10 patients performed by two radiation oncologists and repeated twice. The CT contouring was assisted by a multiparametric MR approach combining a T2-weighted with diffusion-weighted imaging, and a gradient recalled echo for fiducial marker identification. Uncertainty associated to treatment unit was estimated from phantom measurements. The obtained clinical margins were 4.4, 7.3, 5.