BACKGROUND AND PURPOSE: Localisation images normally acquired to verify patient positioning also contain information about the patient's internal anatomy. The aim of this study was to investigate the anatomical changes observed in localisation images and examples of dosimetric consequences. PATIENTS AND METHODS: Localisation images were obtained weekly prior to radiotherapy with an electronic portal imaging device (EPID). A series of 'difference images' was created by subtracting the first localisation image from that of subsequent fractions. Images from 81 lung, 40 head and neck and 34 prostate cancer patients were classified according to the changes observed. Changes were considered relevant if the average pixel value over an area of at least 1cm(2) differed by more than 5%, to allow for variations in linac output and EPID signal. Two patients were selected to illustrate the dosimetric effects of relevant changes. Their plans were re-calculated with repeat CT scans acquired after 4 weeks of treatment and compared with the difference images of the corresponding days. RESULTS: Progressive changes were detected for 57% of lung and 37% of head and neck cancer patients studied. Random changes were observed in 37% of lung, 28% of head and neck and 82% of prostate cancer patients. For a lung case, an increase of 10.0% in EPID dose due to tumour shrinkage corresponded to an increase of 9.8% in mean lung dose. Gas pockets in the rectum region of the prostate case increased the EPID dose by 6.3%, and resulted in a decrease of the minimum dose to the planning target volume of 26.4%. CONCLUSIONS: Difference images are an efficient means of qualitatively detecting anatomical changes for various treatment sites in clinical practice. They can be used to identify changes for a particular patient, to indicate if the dose delivered to the patient would differ from planning and to detect if there is a need for re-planning.