Background: The purpose of this pilot study was to assess the diagnostic accuracy of MR colonography (MRC) without bowel cleansing regarding its ability to quantify inflammatory bowel disease (IBD). In addition, patient acceptance was compared with conventional colonoscopy (CC). Methods: In all, 29 patients with IBD (17 ulcerative colitis; 12 Crohn's disease) were included. While CC was performed after bowel cleansing as the gold standard, MRC was based on a fecal tagging technique and performed 48-72 hours prior to CC. The presence of inflammation in each of 7 ileocolonic segments was rated for every procedure. Patients evaluated both modalities and dedicated aspects of the examination according to a 10-point-scale (1 = good, 10 = poor acceptance). Furthermore, preferences for future examinations were investigated. Results: Inflammatory segments were found by means of CC in 23 and by MRC in 14 patients. Overall sensitivity and specificity of MRC in a segment-based detection were 32% and 88%, respectively. Concerning severely inflamed segments, sensitivity increased to 53% for MRC. Overall acceptance of CC was significantly higher compared to MRC (mean value (mv) for MRT = 6.0; CC = 4.1; P = 0.003). For MRC, the placement of the rectal tube (mv = 7.3), and for CC bowel purgation (mv = 6.5), were rated as the most unpleasant. A total of 67% of patients voted for CC as the favorable tool for future examinations. Conclusions: The presented data indicate that 'fecal tagging MRC is not suitable for an adequate quantification of inflammatory diseases of the large bowel. Furthermore, overall acceptance of endoscopic colonoscopy was superior to MRC.