The purpose of this study was to prospectively compare participant experience and preference of limited preparation computed tomography colonography (CTC) with full-preparation colonoscopy in a consecutive series of patients at increased risk of colorectal cancer. CTC preparation comprised 180 ml diatrizoate meglumine, 80 ml barium and 30 mg bisacodyl. For the colonoscopy preparation 4 l of polyethylene glycol solution was used. Participants' experience and preference were compared using the Wilcoxon signed rank test and the chi-squared test, respectively. Associations between preference and experience parameters for the 173 participants were determined by logistic regression. Diarrhoea occurred in 94% of participants during CTC preparation. This side effect was perceived as severely or extremely burdensome by 29%. Nonetheless, the total burden was significantly lower for the CTC preparation than for colonoscopy (9% rated the CTC preparation as severely or extremely burdensome compared with 59% for colonoscopy; p < 0.001). Participants experienced significantly more pain, discomfort and total burden with the colonoscopy procedure than with CTC (p < 0.001). After 5 weeks, 69% preferred CTC, 8% were indifferent and 23% preferred colonoscopy (p < 0.001). A burdensome colonoscopy preparation and pain at colonoscopy were associated with CTC preference (p < 0.04). In conclusion, participants' experience and preference were rated in favour of CTC with limited bowel preparation compared with full-preparation colonoscopy.