BackgroundLangerhans cell histiocytosis is a rare systemic disease characterized by the abnormal overproduction of histiocytes that tend to infiltrate single or multiple organ systems leading to significant tissue damage. It mainly affects – by order of decreasing frequency – the bone, the skin, the lymph nodes, the liver, and lungs. Gastrointestinal tract involvement is extremely rare in adults.Case presentationWe describe the case of a 32-year-old Middle Eastern man with Langerhans cell histiocytosis involving his lungs and the colorectoanal part of his gastrointestinal tract, with complete resolution of gastrointestinal tract lesions following a non-standardized chemotherapy regimen.ConclusionsGastrointestinal tract lesions are a rare manifestation of Langerhans cell histiocytosis, especially when associated with extraintestinal involvement, such as the lungs. Chemotherapy protocols have not been well established for the treatment of the disease. The clinical impact of the effective chemotherapy regimen used to treat this uncommon presentation of Langerhans cell histiocytosis will be viewed in this case report.Electronic supplementary materialThe online version of this article (doi:10.1186/s13256-017-1428-7) contains supplementary material, which is available to authorized users.