Colon transit time measurement with radio-opaque markers is a method of studying the passage of luminal contents throughout the colon. Overall colonic transit time (CTT), as well as segmental transit times [right (RTT), left (LTT) and rectosigmoid (RSTT)], can be calculated. We hypothesize that CTT is influenced by faecal impaction when the rectum is emptied infrequently. The aim of this study is to investigate the effect of bowel cleansing on colonic transit time in patients with chronic constipation. In 25 women (age 41 years; range 20–65 years) with constipation according to Thompson criteria, CTT measurement was performed in an unprepared situation and repeated after cleansing with 4 L of Klean-Prep®. Ten healthy female volunteers (age 41 years; range 27–57 years) were used as controls. In constipated patients, CTT decreased from a median 70 h (range 10–130 h) to 48 h (5–94 h) in the cleansed state (P < 0.001). A shortening of transit time was found in all three segments. In 10 patients with slow transit (ST) (CTT > 86 h), CTT decreased from 110 h (range 94–130) to 86 (38–94) (P < 0.001). Five of the 10 patients with ST before bowel cleansing had a CTT below 86 h after cleansing. In female controls, uncleansed CTT and RSTT shortened from 39 h (23 to 62) and 17 h (8–29) to 29 h (17–48) and 10 h (0–20) after bowel cleansing (P=0.058 and P=0.046). Colonic intraluminal contents have a substantial effect on colonic transit. In female controls, bowel cleansing shortened rectosigmoid transit. Women with constipation had faster transit in the cleansed state, however, the distribution of markers was not altered. Despite the effect of bowel cleansing on CTT, it seems unnecessary to prepare the bowel in clinical practice because the differentiation of patients between slow transit constipation and outlet obstruction is not changed. However, because in an infrequent defecation pattern, the influence of faecal impaction is considerable, CTT should be applied with care for critical clinical decisions in the treatment of constipation.