Fungi are considered important colonizers of the microbial community, and their proportions and quantities are affected by age, sex, diet, race, region, drugs, diseases and other factors. Intestinal fungi are involved in the human body’s pathophysiological process, and are closely associated with health. In recent years, more and more studies have focused on the colonization of fungi in the digestive tract and their roles in related diseases. At present, evidence shows that the proportions and quantities of intestinal fungi were quite different between healthy people and the patients suffering from tumor,hepatitis, inflammatory bowel disease (IBD), antibiotic-associated diarrhea (AAD), and other disorders. These findings provide new ideas for the further study of intestinal fungi in the diagnosis and treatment of related diseases.