HIS is characterized by colonization of the colonic mucosa of the human distal intestinal tract by Brachyspira spp. Microbiological diagnosis of HIS is not performed, because of the fastidious nature and slow growth of Brachyspira spp. We used a previously described FISH probe to detect and identify Brachyspira spp. FISH allowed rapid visualization and identification of Brachyspira spp. In most cases, the bright FISH signal already allowed rapid localization of Brachyspira spp.