Abstract Background and Aim Although chronic diarrhea is a major digestive disorder, it has not been well studied. The aims of this study were to investigate the prevalence and risk factors of chronic diarrhea in the Japanese population and to assess the relationship between stool type and frequency and symptoms related to chronic diarrhea. Method A total of 13 668 adults who underwent a medical checkup at MedCity21 were enrolled, and 9540 who met the inclusion criteria participated in the study. Participants with chronic diarrhea were defined as those who typically had a Bristol Stool Form Scale of type 6 or 7. Results The prevalence of chronic diarrhea was 3.0%. The risk factors for chronic diarrhea were younger age (odds ratio [OR] 0.984, 95% confidence interval [CI] 0.972–0.996), male sex (OR = 2.270, CI = 1.730–2.960), alcohol intake on ≥5 days per week (OR = 2.390, CI = 1.860–3.060), not getting adequate sleep (OR = 0.712, CI = 0.559–0.907), skipping breakfast ≥3 times a week (OR = 1.490, CI = 1.120–1.980), and absence of diabetes mellitus (OR = 0.384, CI = 0.179–0.824). Only 23.5% of the participants in the diarrhea group had ≥3 bowel movements per day. Chronic diarrhea was significantly associated with heartburn, nausea, stomach ache, abdominal bloating and distension, and feeling of stress. Conclusions Our study shows that chronic diarrhea is common in Japan with a prevalence of 3.0%; unique risk factors related to gender, age, and irregular lifestyle were identified. An understanding of bowel habit in the healthy population is helpful for the assessment of change in bowel habit associated with gastrointestinal disorders.