The aim of the study was to determine prostate set-up accuracy and set-up margins with off-line bony anatomy-based imaging protocols, compared with online implanted fiducial marker-based imaging with daily corrections. Eleven patients were treated with implanted prostate fiducial markers and online set-up corrections. Pretreatment orthogonal electronic portal images were acquired to determine couch shifts and verification images were acquired during treatment to measure residual set-up error. The prostate set-up errors that would result from skin marker set-up, off-line bony anatomy-based protocols and online fiducial marker-based corrections were determined. Set-up margins were calculated for each set-up technique using the percentage of encompassed isocentres and a margin recipe. The prostate systematic set-up errors in the medial-lateral, superior-inferior and anterior-posterior directions for skin marker set-up were 2.2, 3.6 and 4.5 mm (1 standard deviation). For our bony anatomy-based off-line protocol the prostate systematic set-up errors were 1.6, 2.5 and 4.4 mm. For the online fiducial based set-up the results were 0.5, 1.4 and 1.4 mm. A prostate systematic error of 10.2 mm was uncorrected by the off-line bone protocol in one patient. Set-up margins calculated to encompass 98% of prostate set-up shifts were 11-14 mm with bone off-line set-up and 4-7 mm with online fiducial markers. Margins from the van Herk margin recipe were generally 1-2 mm smaller. Bony anatomy-based set-up protocols improve the group prostate set-up error compared with skin marks; however, large prostate systematic errors can remain undetected or systematic errors increased for individual patients. The margin required for set-up errors was found to be 10-15 mm unless implanted fiducial markers are available for treatment guidance.