Choledochal cyst is a relatively uncommon entity in Western countries. No reports of choledochal cyst in heart transplant patients have been reported to date. We report two cases of choledochal cyst in pediatric heart transplant recipients, one with post-transplant lymphoproliferative disorder (PTLD) within the cyst. The first patient had abdominal pain, increased liver enzymes and was seropositve for Epstein-Barr virus. A choledochal cyst with PTLD was removed 4 years after heart transplantation. The second patient presented 14 years after heart transplantation with a choledochal cyst that was excised for severe abdominal pain. This previously unreported association between choledochal cysts in conjunction with PTLD and heart transplantation is interesting and a possible common pathogenesis is proposed. The management and alternative treatments were briefly noted. We recommend an aggressive treatment for patients with suspected choledochal cyst after heart transplantation because of the increased potential for malignant transformation.