Langerhans cell histiocytosis (LCH) is a rare disease of unknown etiology characterized by oligoclonal proliferation of Langerhans cells. The diagnosis of LCH is complicated by the fact that it may involve multiple organ systems and its clinical presentation and course varies, ranging from an isolated to a multisystem disease. We report a 35-year-old male with LCH involving multiple systems, including the bones, lungs, spleen, liver and bile ducts, whose first clinical presentation was liver dysfunction. The patient was diagnosed following a skull biopsy that revealed infiltration of Langerhans cells. However, a liver biopsy revealed sclerosing cholangitis (SC) with no signs of Langerhans cell infiltration, and the clinical manifestations of the involved organs were atypical, leading to a delayed diagnosis. The patient was in partial remission following chemotherapy. In conclusion, findings of this case may aid our understanding of the pathophysiology of LCH and in improving its diagnosis and treatment.