This paper aims to quantify changes in colonic length and positional change between supine and prone CT colonography (CTC) studies in order to aid development of image registration techniques. CTC studies in 20 patients (10 men and 10 women) with technically adequate distension were analysed using an image analysis workstation. Spatial co-ordinates of colonic landmarks were determined in both prone and supine orientations using a three-dimensional colon model view and centreline positions. Change in the co-ordinate position of colonic segments between supine and prone scans was calculated using the superior mesenteric artery as a fixed point of reference. There was no significant difference in total colonic length for subjects between prone and supine positions, nor any significant difference overall when men were compared with women. However, significant differences between sexes for individual segments were found; the ascending colon, descending colon and rectum were significantly longer in men and the sigmoid colon was longer in women. The transverse colon was the most mobile segment during positional change, with an average displacement between supine and prone scans of 4.6 cm (standard deviation, 0.48 cm) for men and 4.1 cm (standard deviation, 0.4 cm) for women. Consistent patterns of colonic positional change between supine and prone orientations were present and were thought to be most likely the result of abdominal compression. We concluded that there is minimal variation in colonic length between prone and supine orientations. Consistent patterns of colonic displacement with patient position suggest that predictable forces act upon the colon. Understanding these forces will facilitate image registration for CT colonography.