The spectrum of congenital intrahepatic diseases described in canine and feline patients is broad, and the etiopathogenesis is complex. Developmental dysregulation of the intrahepatic biliary tree and vasculature leads to malformations of the ductal plate and aberrant vascular connections. Occasionally, intrahepatic congenital disorders occur as a constellation of biliary and vascular anomalies. Diagnosis requires clinical data, advanced diagnostic imaging, and, in the case of hepatic fibropolycystic disease, liver histopathology. Clinical prognosis is variable.