Irritable bowel syndrome (IBS) is a disorder of chronic abdominal pain, altered bowel habit and abdominal distension. It is the commonest cause of referral to gastroenterologists in the developed world and yet current therapeutic strategies are often unsatisfactory. There is now increasing evidence linking alterations in the gastrointestinal (GI) microbiota and IBS. Changes in faecal and mucosa-associated microbiota, post-infectious IBS, a link with small intestinal bacterial overgrowth and an up-regulation of the GI mucosal immune system all suggest a role for the GI microbiota in the pathogenesis of IBS. Given this evidence, therapeutic alteration of the GI microbiota by probiotic bacteria could be beneficial. The present paper establishes an aetiological framework for the use of probiotics in IBS and comprehensively reviews randomised placebo-controlled trials of probiotics in IBS using multiple electronic databases. It highlights safety concerns over the use of probiotics and attempts to establish guidelines for their use in IBS in both primary and secondary care.