Therapeutic effect of fecal microbiota transplantation (FMT) was assessed using common marmosets as a nonhuman primate model. FMT therapy resulted in ameliorating diarrhea, weight loss, hypoalbuminemia and anemia in some chronic diarrhea cases of marmosets. FMT also tended to cure recurrent Clostridium difficile infection in marmosets. Analysis of fecal bacterial flora based on the 16S rRNA gene showed shifts of bacterial composition in the animals after FMT, implying that FMT therapy cured dysbiosis related to these intestinal diseases.