Gut microbiota dysbiosis including small intestinal bacterial overgrowth (SIBO) received increasing attention recently; this has resulted from increasing number of publications on relationship between gut microbiota and gastrointestinal (GI) function, pathogenesis of several digestive and extra-digestive diseases, and potential value of different gut microbiota modifying modalities (e.g. probiotics, antibiotics, and fecal microbiota transplantation) to treat these conditions. Conventionally, a total bacterial count >105 colony forming units (CFU) per mL of upper gut aspirate is considered diagnostic of SIBO. Recently, even a total bacterial colony count of >103 CFU per mL of upper gut aspirate has been considered as low-grade SIBO, which has been shown to be of clinical significance. In spite of the fact that quantitative upper gut aspirate culture is considered “gold standard” test for the diagnosis of SIBO, its limitations include invasiveness, need for microbiology back up, and inability to culture 70% gut bacteria. With availability of non-invasive breath tests for diagnosis of SIBO such as breath tests, there has been considerable amount of data in the literature on SIBO in various diseases. Malabsorption syndrome, parasitic infection of gastrointestinal tract, persistent diarrhea and malnutrition in children, inflammatory bowel disease particularly Crohn disease, irritable bowel syndrome, achlorhydria due to atrophic gastritis, proton pump inhibitor therapy or gastric surgery, jejunoileal bypass surgery, gut neuromyopathy, intestinal stricture, short bowel syndrome, non-alcoholic steatohepatitis, cirrhosis of liver, old age, and small intestinal diverticulosis etc. are associated with SIBO. SIBO is diagnosed by invasive tests such as quantitative culture of upper gut aspirate and non-invasive hydrogen breath test. Treatment of SIBO is directed to the cause of SIBO and broad spectrum antibiotics, particularly rifaximin.