PURPOSE To evaluate the magnitude of systematic and random errors from a subset of 100 prostate and 26 head and neck (H&N) cancer patients treated with conventional conformal radiotherapy and using image-guided radiotherapy (IGRT). After treatment, the uncertainties involved and the CTV to PTV margin were evaluated. MATERIAL AND METHODS An Elekta Synergy® linear accelerator was used, taking advantage of 3D on-board computed tomography. IGRT with no-action level (NAL) protocol was applied, reporting the 3D translation and rotation corrections. A statistical study was performed to analyse systematic, random and interobserver uncertainties, and, finally, to obtain the CTV to PTV margins. RESULTS The H&N patients' uncertainties found were smaller than those of prostate patients. The CTV to PTV margins assessed, following the guidelines found in the literature, in the three dimensions of space (right-left, superior-inferior, anterior-posterior) were (5.3, 3.5, 3.2) mm for H&N and (7.3, 7.0, 9.0) mm for prostate cancer treatments. CONCLUSIONS It was found that assessing all the involved uncertainties within radiation treatments was very revealing; their quality improves using IGRT techniques and performing extensive data analysis.