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Abstract Autoimmune sclerosing cholangitis is an overlap syndrome characterized by features of both autoimmune hepatitis and primary sclerosing cholangitis, the latter usually involving the large bile ducts. Autoimmune sclerosing cholangitis occurs more often in children than in adults and is frequently associated with inflammatory bowel disease, predominantly ulcerative colitis. We report a unique case of a 10-year-old Danish boy with severe small duct autoimmune sclerosing cholangitis and synchronic Crohn colitis. He was referred with a history of weight loss, abdominal pain, vomiting and diarrhea. Biochemical anomalies included elevated alanine aminotransferase, γ-glutamyl transferase and immunoglobulin G levels and the presence of smooth muscle antibodies and perinuclear antineutrophil cytoplasmic antibodies but normal alkaline phosphatase. Liver biopsy specimen revealed features of both autoimmune hepatitis and sclerosing cholangitis, the latter characterized by acute, hyperplastic and destructive inflammation – granulocytic epithelial lesion – of the small ducts. Magnetic resonance cholangiography was normal. Colonoscopic biopsies showed chronic inflammatory changes of the caecum and the ascending and transverse colon compatible with Crohn disease. Ursodeoxycholic acid and immunosuppressive treatment was initiated and within four weeks of treatment the general condition improved. Normalization of aminotransferase was seen at 21 weeks and γ-glutamyl transferase at 72 weeks after first admittance, while immunoglobulin G remained slightly increased. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1418596609736470