IntroductionTo quantify interfraction patient setup-errors for radiotherapy based on cone-beam computed tomography and suggest safety margins accordingly.Material and MethodsPositioning vectors of pre-treatment cone-beam computed tomography for different treatment sites were collected (n = 9504). For each patient group the total average and standard deviation were calculated and the overall mean, systematic and random errors as well as safety margins were determined.ResultsThe systematic (and random errors) in the superior-inferior, left-right and anterior-posterior directions were: for prostate, 2.5(3.0), 2.6(3.9) and 2.9(3.9)mm; for prostate bed, 1.7(2.0), 2.2(3.6) and 2.6(3.1)mm; for cervix, 2.8(3.4), 2.3(4.6) and 3.2(3.9)mm; for rectum, 1.6(3.1), 2.1(2.9) and 2.5(3.8)mm; for anal, 1.7(3.7), 2.1(5.1) and 2.5(4.8)mm; for head and neck, 1.9(2.3), 1.4(2.0) and 1.7(2.2)mm; for brain, 1.0(1.5), 1.1(1.4) and 1.0(1.1)mm; and for mediastinum, 3.3(4.6), 2.6(3.7) and 3.5(4.0)mm. The CTV-to-PTV margins had the smallest value for brain (3.6, 3.7 and 3.3mm) and the largest for mediastinum (11.5, 9.1 and 11.6mm). For pelvic treatments the means (and standard deviations) were 7.3 (1.6), 8.5 (0.8) and 9.6 (0.8)mm.ConclusionsSystematic and random setup-errors were smaller than 5mm. The largest errors were found for organs with higher motion probability. The suggested safety margins were comparable to published values in previous but often smaller studies.