The authors retrospectively evaluated the setup uncertainties in Intensity-Modulated Radiation Therapy (IMRT) for pituitary adenomas and verified the margins used in daily practice (3 mm). Craniocaudal (CC), anteroposterior (AP) and laterolateral (LL) displacements were measured during the first 3 days of treatment and then weekly by comparing two orthogonal images obtained by an electronic system of portal imaging with Digitally Reconstructed Radiographs (DRRs). Setup Margins (SM) were defined according to the International Commission on Radiation Units (ICRU)-62 formula, the Stroom equation and the van Herk equation. The systematic (Σ) and random (σ) errors of the population were calculated as standard deviation (SD) of the population mean and the mean of SDs for every patient, respectively. Twenty patients were treated by IMRT for pituitary adenomas, and a total of 231 measurements were obtained. Σ and σ were 0.6 and 1.3 mm, 0.8 and 1 mm, 1.2 and 1.5 mm in the AP, LL and CC direction, respectively. Larger setup margin was 2.4, 2.7 and 4 mm in the AP, LL and CC direction, respectively (van Herk formula). IMRT is a highly sophisticated treatment technique that requires precise definition and optimisation of local setup errors and, finally, of the irradiated volumes. The role of image-guided RT in these kinds of treatments should be prospectively evaluated.