Banana is a widely consumed fruit, which contains considerable amounts of potential prebiotic indigestible carbohydrates. In our randomised, controlled trial we aimed to evaluate the in vivo prebiotic effect of banana consumption on faecal microbiota. Thirty-four healthy women participated in the study, having Body Mass Index (BMI) 24-30 kg/m(2), age 19-45 years, without history of gastrointestinal disease and no antibiotic and other medication use two months prior the initiation and during the study. All women were asked to maintain their usual dietary habits for 60 days and they were randomly assigned to consume twice a day a pre-meal snack, either one medium banana, or one cup of banana-flavoured drink or one cup of water (control group). Stool samples were collected at baseline, on days 30 and 60 of intervention for enumeration of total anaerobes, bifidobacteria and lactobacilli by plate count techniques, as well as for pH and short chain fatty acids (SCFAs) measurement. Gastrointestinal symptoms were also recorded. Mean bifidobacterial levels were increased only in the banana group both at 30 and 60 days of intervention, but this change did not reach a statistical significance. No significant overall differences in the total concentrations and molar ratios of SCFAs were detected according to dietary intervention. Analysis of the gastrointestinal symptoms records revealed significantly lower bloating levels in the banana group, compared to controls, at 26-35 days (p = 0.009) and 51-60 days (p = 0.010). Banana consumption had also no adverse effects on evacuation patterns. We concluded that daily consumption of bananas is a well-tolerated eating behaviour, which may induce bifidogenesis in healthy women experiencing body weight problems.