A 38-year-old heterosexual male presented with a 6 to 7 week history of severe diarrhoea but no other complaints. In routine faecal cultures and routine parasitological investigations no pathogenic micro-organisms were observed. Colonoscopy revealed a normal mucosa. Multiple biopsies were obtained. The histological diagnosis was invasive intestinal spirochaetosis. The immunostain for Borrelia burgdorferi cross-reacted with the spirochetes of the intestinal spirochaetosis. After two weeks of incubation under strict anaerobic conditions a spirochaete was cultured from a biopsy of the sigmoid mucosa. The 16SrDNA sequence was consistent with Brachyspira aalborgi. The HIV and syphilis results were negative. The patient was treated first with metronidazole and then by clindamycin. The diarrhoea subsided after the second course of treatment and the cause was presumed to have been the invasive intestinal spirochaetosis. Intestinal spirochaetosis is usually found coincidentally at histological examination of colon biopsies. There is no general consensus that intestinal spirochaetosis is the cause of the diarrhoea. There is however an association between the presence of symptoms and the invasivity of spirochaetes, morphological colon epithelial changes and evidence of immune response. The literature reports patients who improve symptomatically without specific treatment. Treatment may be given to patients with severe symptoms.