With the development of “Human Microbiome Project” and “Metagenomics of the Human Intestinal Tract”, great attention has been paid on human gut microbiota. With the increasing knowledge of the composition and function of gut microbiota, we found that gut microbiota play an important role on human health, and can be regarded as “the forgotten organ”. The recent researches have showed that diseases such as Parkinson's disease, breast cancer, HIV, hepatic cirrhosis, renal disorder, arthrophlogosis, diabetes are related to the dysfunction of gut microbiota. Several studies also revealed the effects of sweetening agents, emulsifying agents and diet on health by concerning the role of gut microbiota. Moreover, gut microbiota have become a new point of view for the investigation on the beneficial mechanism of dietary factors including probiotics, prebiotics, essential elements, and polyphenols. With the development of related researches, gut microbiota may become the biomarkers for the prediction and diagnosis of diseases. The pathogenesis and protective mechanisms of diseases and healthy food respectively can also be better explained by evaluating the effects of gut microbiota on human health.