Very low-carbohydrate diets are often used to promote weight loss, but their effects on bowel health and function are largely unknown. We compared the effects of a very low-carbohydrate, high-fat (LC) diet with a high-carbohydrate, high-fibre, low-fat (HC) diet on indices of bowel health and function. In a parallel study design, ninety-one overweight and obese participants (age 50·6 (sd 7·5) years; BMI 33·7 (sd 4·2) kg/m2) were randomly assigned to either an energy-restricted (about 6–7 MJ, 30 % deficit) planned isoenergetic LC or HC diet for 8 weeks. At baseline and week 8, 24 h urine and faecal collections were obtained and a bowel function questionnaire was completed. Compared with the HC group, there were significant reductions in the LC group for faecal output (21 (sd 145) v. − 61 (sd 147) g), defecation frequency, faecal excretion and concentrations of butyrate ( − 0·5 (sd 10·4) v. − 3·9 (sd 9·7) mmol/l) and total SCFA (1·4 (sd 40·5) v. − 15·8 (sd 43·6) mmol/l) and counts of bifidobacteria (P < 0·05 time × diet interaction, for all). Urinary phenols and p-cresol excretion decreased (P ≤ 0·003 for time) with no difference between diets (P ≥ 0·25). Faecal form, pH, ammonia concentration and numbers of coliforms and Escherichia coli did not change with either diet. No differences between the diets were evident for incidences of adverse gastrointestinal symptoms, which suggests that both diets were well tolerated. Under energy-restricted conditions, a short-term LC diet lowered stool weight and had detrimental effects on the concentration and excretion of faecal SCFA compared with an HC diet. This suggests that the long-term consumption of an LC diet may increase the risk of development of gastrointestinal disorders.