The human intestinal microbiota is made up of trillions of microorganisms that are considered to be nonpathogenic. The microbiota functions in tandem with the host’s defences and the immune system to protect against pathogen colonisation and invasion. It also performs an essential metabolic function, acting as a source of essential nutrients and vitamins and aiding in the extraction of energy and nutrients, such as short-chain fatty acids (SCFA). Gut microbiota alterations are being increasingly recognized as an important factor in the pathogenesis and pathophysiology of irritable bowel syndrome (IBS). Irritable bowel syndrome is a disease with a complex and unknown etiology. It is a functional disease although many researchers regard it as chronic, due to the long duration or frequent recurrence. IBS is characterized by abdominal pain and disturbances in bowel habits (constipation and/or diarrhea), in the absence of pathological organic changes. Studies in recent years have shown a significant effect of the intestinal microflora and intestinal cerebrospinal axis in the pathogenesis of the disease. Modulation of th intestinal microflora using probiotics and the focus on the function of uncultured intestinal microbiota will offer new opportunities for treatment of patients with this syndrome. Research into the intestinal microflora (the properties of microorganisms) is a promising direction, allowing for further understanding and characterization of many bacteria responsible for the pathophysiology and symptoms of IBS. It is still an enigmatic disease of multifactorial etiology, which seems to be related in significant ways to the composition of the intestinal microbiota. Research on the use of probiotics and prebiotics in IBS should be continued in numerous, well-planned clinical trials in order to obtain the best results in reducing IBS symptoms