A 10-month-old, previously healthy boy presented with one week of mild jaundice, light-colored stools and irritability. Abdominal sonography showed a large type I choledochal cyst and a separate, distinct cystic mass at the head of the pancreas. Magnetic resonance cholangiopancreatography was performed to evaluate the relationship of the two lesions. A type I choledochal cyst was confirmed, and a coexisting type III choledochocele was identified as the second cystic structure in conjunction with pancreaticobiliary malunion. The infant had complete resection of the type I choledochal cyst with Roux-en-Y hepaticojejunostomy, and anterior duodenotomy with marsupialization of the choledochocele. After five years of follow-up, the child is thriving and has had no recurrence of his symptoms. An exhaustive review of the literature identifies only one previous case of synchronous types I and III choledochal cysts, and this association is not clearly defined among the traditional classifications of type IV multiple choledochal cysts. Because operative management of a type III cyst requires the addition of a transduodenal approach, we encourage accurate reporting of mixed type choledochal cysts for the benefit of surgical planning, epidemiologic tracking and outcomes.