The purpose of this paper is to assess colonic distension and length and to evaluate a polyp matching algorithm on prone and supine studies in CT colonography (CTC) computer aided diagnosis (CAD). Our CTC CAD software was used to reconstruct the colonic surface, to compute the colon centerline and to detect spatial positions of polyps. Normalized distance along the centerline (NDAC) and colon distension at each polyp were compared in prone and supine positions. 8 patients presented 12 polyps detected in both supine and prone positions and confirmed by colonoscopy. NDAC for all polyps were very similar in supine/prone positions. The average NDAC differences were 0.01 ± 0.01 which indicates excellent agreement. Colon profiles (distension vs. DAC) were not similar in supine/prone positions due to high variability of colonic distension and mobility of the colon when the patient was repositioned. However the final colon lengths and average distension were very similar (average difference was 4.5%). Also, as could be expected from normal anatomy, the cecum and rectum tended to have the greatest distension and the rectum tended to be better distended on the prone exam. The colon centerline provides a natural coordinate reference and is a useful tool for CTC CAD.