There has been an increasing interest in the association between human disease and altered gut microbiota, and therapeutics to modulate microbiota to treat disease. Healthy human gastrointestinal microbiota is highly diverse and rich, and harbors between 500 and 2,000 species. Diseases associated with dysbiotic microbiota include antibiotic‐associated diarrhea, Clostridium difficile infection, multidrug‐resistant organisms, inflammatory bowel disease, obesity, metabolic syndrome, diabetes mellitus, neuropsychiatric diseases, and systemic autoimmune diseases. Microbiota replacement therapies have shown immense promise in treatment of recurrent C. difficile infection and are being studied for other indications. Microbiota replacement therapies for indications other than C. difficile infection should be performed only in research settings. There is an immense need for standardized microbiota replacement therapies for C. difficile infection. Studies are needed to elucidate long‐term safety and adverse events from these therapies.