In a 27-year-old patient suffering from Crohn’s disease covering nearly the entire small intestine, the major problem was a marked protein-losing enteropathy which required long-term intravenous replacement. Accidentally, we disclosed a dilated thoracic duct with incompetent valves and stenosis at the junction into the subclavian vein in this patient. To reduce the intestinal protein loss, an anastomosis was performed between the thoracic duct and the internal jugular vein. Subsequently the intestinal protein loss dropped from 40 to 26% and replacement of proteins could be reduced. The patient was observed for 4 years postoperatively and the therapeutic effect continued. Besides this therapeutic aspect, the present case gives cause to consider the possible role of the lymphatics in the pathogenesis of Crohn’s disease.