The gut microbiota is involved in the maintenance of humans' health and its alterations have been associated to several intestinal and extra intestinal disorders. For this reason, there is increasing interest on gut microbiota modulation as both a preventive strategy or as a therapeutic option in different gastrointestinal, hepatic and systemic diseases. Many studies have tried to find out the impact of diet, prebiotic, probiotic and antibiotics on gut microbiota composition and function, obtaining very heterogeneous and sometimes conflicting results, especially as regards the effect on clinical outcomes. However, these preliminary data represent a promising premise for further studies that will provide a more comprehensive knowledge about the role of gut microbiota as a therapeutic target.