OBJECTIVE We describe an exceptional case of Langerhans cell histiocytosis (LCH) that presented as Crohn's disease and primary sclerosing cholangitis. METHODS The patient's clinical, endoscopic, and histologic data from the Centre Hospitalier de l'Universite de Montreal were reviewed, as well as the literature on LCH involving the digestive tract and the liver, with a focus on the similarities with Crohn's disease and primary sclerosing cholangitis. RESULTS A 39 years-old man first presented with anal fissures and deep punctiform colonic ulcers. Histologic assessment of colon biopsies showed chronic active colitis, consistent with Crohn's disease. Mild cholestasis and endoscopic retrograde cholangiopancreatography (ERCP) showing multiple intra and extrahepatic biliary tract strictures also led to a diagnosis of sclerosing cholangitis. Perianal disease progressed despite conventional treatment with antibiotics and infliximab. Subsequent discovery of non-Langerhans cutaneous xanthogranulomas and panhypopituitarism raised the suspicion of LCH, and a second review of colon biopsies ultimately led to the diagnosis, with the identification of Langerhans cells depicting elongated, irregular nuclei with nuclear grooves as well as immunohistochemical reactivity for S100, CD1a and vimentin. BRAF V600E mutation was detected afterwards by DNA sequencing of a bile duct sample. CONCLUSIONS LCH may mimic inflammatory bowel disease (IBD) and must be suspected in the presence of other suggestive clinical signs, or when there is failure of conventional IBD treatment.