The aim of this study was to compare optical colonoscopy to fecal-tagging-based MR colonography in a screening population in terms of comfort and acceptance ratings as well as for future preferences as colorectal cancer screening examinations. Two hundred eighty-four asymptomatic patients (mean age 59 years) underwent MRC and OC within 4 weeks. While MRC was based on a fecal tagging technique, OC was performed after bowel cleansing. For OC, sedatives and analgesics were used. Patients evaluated both modalities and certain aspects of the examination according to a 10-point-scale with higher scores denoting a worse experience. Furthermore, preferences for future examinations were evaluated. No significant difference was noted for the overall acceptance of OC (mean value 3.0) and MRC (mean value 3.4). For MRC, the placement of the rectal tube was rated as the most unpleasant part, whereas bowel purgation was regarded most inconvenient for OC. Patients aged 55 years and older perceived most aspects less unpleasant than younger patients. Of the patients, 46% preferred MRC for future screening examinations (OC: 44%). OC and MRC have comparable general acceptance levels in a screening population. Especially for patients declining endoscopy as a screening method MRC may evolve as an attractive alternative.