Objective. Information on the relationships between stool characteristics and colonic transit time (CTT) in irritable bowel syndrome (IBS) is limited. Our aims were: (i) to relate stool frequency and consistency to total and segmental CTTs, (ii) to correlate changes in these stool characteristics with changes in CTTs between a baseline assessment and a 12-week assessment, and (iii) to examine the confounding effects of mood on these relationships, in patients with IBS. Materials and methods. Twenty-one female patients with IBS underwent, on two occasions 12 weeks apart, a colonic transit study and completed at these times Bristol Stool Form Scale (BSFS) and Bowel Symptoms Severity Rating Scale (BSSRS). All patients also completed the Hospital Anxiety and Depression scale. Results. Between baseline and the 12-week assessment, an increase in the number of days over the past week without a bowel motion correlated with prolonged total CTT (r = 0.54, p = 0.01). An increase in the number of days with more than three bowel motions per day correlated with a shorter right CTT (r =-0.52, p = 0.02). Only after adjusting for anxiety and depression, did an increase in loose or watery bowel motions (for BSSRS but not for BSFS) correlate with a shorter right CTT (r =-0.47, p = 0.03). Conclusions. Stool frequency, as well as stool consistency, correlates with CTT. Correlations between stool consistency and CTT are more robust for BSSRS than for BSFS. An effect of mood appears to be important in the relationship between stool consistency and CTT.