The human colon is home to a microbial ecosystem that enhances resistance to infection, stimulates mucosal immune defenses, synthesizes essential vitamins, and promotes caloric uptake by hydrolyzing complex carbohydrates. Clinical and experimental studies demonstrated that the colonic microbiota play an essential role in enhancement or reduction of intestinal and systemic inflammatory diseases. Because of its potential to protect against invasion by pathogens, targeted manipulation of microbial populations is a growing focus of investigation as a therapeutic strategy to manage several gastrointestinal disorders. But at the moment there are some legal problems that cause this method cannot widely used for patients. United State FDA has not yet completely approved the procedure and only patients who do not respond to other treatment options, are able to use fecal microbiota transplantation (FMT). However considerable research is required to evaluate the FMT in order to optimize this therapeutic process protocols before using this therapy.