Cyriel Ponsioen’s research focuses on chronic inflammatory diseases of the bowel (ulcerative colitis and Crohn's disease) and of the bile ducts (particularly primary sclerosing cholangitis (PSC). He mainly studies the role of the gut flora – microbiota – in the development and management of these disorders. An important therapeutic model for these disorders involves faecal transplantation (stool transplants) as the most radical way of restoring the disturbed gut flora in people who suffer from these chronic inflammatory diseases. Regarding PSC, Ponsioen's research mainly focuses on epidemiology, disease course, and the development of biomarkers for this. He is also leading a line of research into the relationship between the bowel and the bile ducts and the possibilities for drug treatment at this level.