The present invention relates to the use of fecal matter in the treatment of a subject having autoimmune disease, wherein the fecal matter is autologous to the subject, and preferably administered to the small intestine, preferably the duodenum, of the subject. The fecal matter can be one or more constituents of autologous feces, preferably chosen from the group consisting of bacteria, viruses, bacteriophages, fungi, metabolites, microRNAs, proteins, antibodies, and/or antigens.
