The increased risk of developing irritable bowel syndrome (IBS) following gastroenteritis and the co-existence of dysbiosis, elevated luminal gas production and immune activation, indicate that the gastrointestinal microbiota may be a therapeutic target in IBS. Following increasing numbers of randomised controlled trials (RCTs), the low FODMAP diet has become widely used as a successful approach to reducing symptoms in IBS, but also dramatically impacts on the gut microbiota. In part, this is likely related to the reduction in prebiotic fructans and galacto-oligosaccharides. Prebiotics are non-digestible, fermentable food components that result in ‘the selective stimulation of growth and/or activity of one or a limited number of microbial genera/species in the gut microbiota that confer health benefits to the host’. In contrast to the low FODMAP diet there are a small number of studies that actually supplement prebiotics with the aim of managing IBS symptoms. There are very few controlled trials of prebiotics in IBS. Two studies of 6-20 g/d of fructans found no differences in symptoms following the intervention or control, whereas a trial of 3.5 g/d of GOS resulted in improvement in global IBS symptoms, bloating and flatulence, whereas a higher dose did not. These preliminary studies suggest that low doses of some specific prebiotics may improve symptoms of IBS, although further robust clinical trials are required.