Background Pigmented bile salts darken the small-bowel lumen and are present with bile acid, which is involved in the development of bowel habits. The small-bowel water content (SBWC) in the ileum could represent the colonic environment, although no studies have focused on this feature. However, measurement of the crude SBWC can be challenging because of the technical difficulty of the endoscopic approach without preparation. Our aim was to evaluate optically active bile pigments in the SBWC of patients with abnormal bowel habits using capsule endoscopy (CE), to investigate the impact of bile acid on bowel habits. In addition to conventional imaging, we used flexible spectral imaging color enhancement (FICE) setting 1 imaging, in which the effects of bile pigments on color are suppressed.Methods The study population included 37 constipated patients, 20 patients with diarrhea, and 77 patients with normal bowel habits who underwent CE between January 2015 and May 2018. Patients with secondary abnormal bowel habits were excluded. Intergroup color differences of SBWC in the ileum (ΔE) were evaluated from conventional and FICE setting 1 images. Color values were assessed using the CIE L*a*b* color space. Differences in lightness (black to white, range 0 to 100) of SBWC were also evaluated.Results Values of ΔE calculated from comparisons of conventional images of constipated and normal-bowel-habit patients, and patients with diarrhea and normal-bowel-habit patients were 11.3 and 10.7, respectively. These values decreased to 3.9 and 3.2, respectively, when FICE setting 1 images were evaluated. The SBWC lightness of patients with constipation and diarrhea was significantly brighter (34.0 versus 27.2, P < .0001) and darker (18.8 versus 27.2, P < .0001), respectively, compared with the normal-bowel-habit patients. Examination of the FICE setting 1 images did not reveal significant differences in SBWC lightness between the constipated and normal-bowel-habit groups (44.7 versus 46.7, P = .33) or between the diarrhea and normal-bowel-habit groups (44.7 versus 42.3, P = .39).Conclusions Differences in color and darkness of the SBWC in the ileum appear to be attributable to bile pigments. Therefore, bile pigments in SBWC could reflect bowel habits.