A 12-year-old girl presented with a protein-losing enteropathy. Symptoms started 4 weeks after undergoing the Fontan procedure at the age of 1.5 years for mitral atresia, ventricular septal defect, and double-outlet right ventricle. Upon referral for 3 weeks of rehabilitation after multiple interventional measures and drug treatments, she appeared in a dystrophic state, with decreased plasma protein and electrolyte levels along with occasional tetanic convulsions. Blood glucose levels after a lactose tolerance test were markedly reduced. The introduction of a lactose-free diet was quickly effective, with plasma protein and electrolyte levels raised to normal levels, and the girl's body weight increased without ascites or oedema. Molecular genetic examination revealed a homozygous C/C13910 polymorphism in the LCT gene. Conclusion: Protein-losing enteropathy in the Fontan circulation may be provoked by lactase deficiency and should therefore be ruled out to exclude this rather common condition.