This study compared a standard PEG protocol with a bowel cleansing by low-pressure water infusion into the colon (Prep System, Lifestream®, Austin, TX). 104 patients were randomly assigned to either a split-dose 2 L+2 L PEG or the Prep System, after 5 days low residue diet. Prep System cleansing consisted of infusion of 2 × 35 L water at 37°C, by gravity into the rectum, over one hour. Quality of bowel cleansing was assessed with the Boston bowel prep score (BBPS) by a colonoscopist who was blinded to the pre-procedural preparation. Groups were comparable for age, sex and colonoscopy indication. The total median (7 in both groups), and segmental BBPS scores were not different between groups. Mean duration of colonoscopy, blood electrolytes after bowel cleansing and patient satisfaction (89% in the prep system and 76% in the PEG) were not different in the 2 groups. Adverse events, mainly nausea, were more frequent in the PEG group (P=0.03). In the setting of this study, the prep system appeared as effective as the split-dose PEG for bowel cleansing before colonoscopy. Patient tolerance of the prep system was good.