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Rhabdomyosarcoma is a soft tissue malignant tumor affecting 1% of children from 0 to 14 years. Preoperative imaging may not always be diagnostic for hepatobiliary rhabdomyosarcoma and differential diagnosis with choledochal cyst (CC) could be difficult. We report a case of 2-years-old girl with a strange CC pattern of presentation. A grapelike lesion involving the choledochal and biliary ducts was easily and completely resected by robotic assisted surgery. Since no previous reports were available about oncologic safety of robotic approach, the porto-enterostomy was performed in open surgery. On histologic examination, the specimen revealed a botryoid-embryonal rhabdomyosarcoma affecting both the common bile duct and the common hepatic duct. One year postoperatively the child is safe of tumor relapse. Robotic approach seems to be safe and advantageous to obtain a radical excision of the tumor at the porta hepatis, even in case of misdiagnosed malignant lesion mimicking a CC.