Protein-losing enteropathy is a well-known complication after the Fontan procedure, and unfractionated heparin therapy has been tried with some success as a potential therapy. Low-molecular weight heparin is believed to be ineffective. We now describe a case in which an adult patient with protein-losing enteropathy after Fontan palliation was successfully treated with systemic doses of low-molecular weight heparin, with complete resolution in the 24-hour fecal alpha-1 anti-trypsin level and serum albumin. The patient continues to remain in remission with this therapy. In conclusion, these findings are novel and compel us to re-evaluate our pathophysiologic understanding of this difficult condition.