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Overweight has recently been shown to accelerate small bowel transit. The role of gut transit and body weight in idiopathic bile acid malabsorption (IBAM) is unclear. We have prospectively studied gastrointestinal transit and body mass index (BMI) in patients with IBAM.One hundred and ten patients with chronic diarrhea were prospectively included for transit measurements. All patients underwent a gastroscopy and colonoscopy, 75SeHCAT test for detection of bile acid malabsorption and calculation of BMI. Forty-three patients (15 men) had IBAM. A newly developed radiological procedure was used to measure gastrointestinal transit during one visit. The results were compared to results obtained in 83 healthy subjects.Colonic transit in women with IBAM was 0.8 (0.3–1.5) days versus 1.5 (1.0–3.7) days in healthy women (median and percentile 10 and 90; p < 0.0001). In men with IBAM it was 0.8 (0.1–1.0) days; in healthy men it was 1.3 (0.8–1.9) days, p < 0.0001. Segmental colonic transit was accelerated only in the distal colon in men and women with IBAM compared with healthy subjects. Small bowel transit time in women with IBAM was 1.9 (1.1–3.0) h versus 3.3 (1.5–6.3) h in healthy women, p = 0.0002. In men with IBAM it was 2.1 (1.2–3.2) h and 2.5 (1.4–4.3) h in healthy men (p = 0.04). BMI in patients with IBAM was 27.3 (20.4–33.8) kg/m2 and in healthy subjects it was 23.8 (20.5–26.2) kg/m2, p < 0.0001.Accelerated small bowel and distal colonic transit as well as overweight are probably involved in the pathophysiology of IBAM.