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Exact prevalence and annual incidence data are not available for CD, but the disease is known to be very rare. An estimated prevalence of 1/1,000,000 has been suggested. There is a slight female gender bias.

Caroli disease can present at any age. CD ranges from simple ectasias of the larger intra-hepatic bile ducts (in this less common form the name Caroli disease is used) to a syndromic form (Caroli syndrome) that is more common and includes congenital hepatic fibrosis. Some patients remain asymptomatic throughout the disease course. Some develop intra- or extra-hepatic calculi, leading to recurrent cholangitis (with bacteremia and sepsis), and acute pancreatitis. Manifestations are those of complications, mostly bacterial cholangitis, and include abdominal pain and biliary colic, fever with chills, and jaundice. Hepatomegaly, cirrhosis and portal hypertension (with splenomegaly) are also frequently reported to develop. Besides bacterial cholangitis, complications include liver abscess, biliary infection, and in late stages, cholangiocarcinoma. CS is often associated with recessive polycystic kidney disease (see these terms). The course is largely dependent on the associated disorders.

CD and CS are strongly related to PKHD1 mutations. Abnormal development of the embryonic bile ducts at the stage of ductal plate has been suggested. Full characterization of genetic anomalies associated with CD or CS beyond PKHD1 has not yet been achieved.

The diagnosis is suspected on clinical grounds and confirmed through detection of cystic dilatation in the biliary tree through imaging studies. The key diagnostic procedure is magnetic resonance cholangiography showing a characteristic aspect of abnormal bile ducts. Endoscopic retrograde cholangiopancreatography (ERCP) and percutaneous transhepatic cholangiography (PTC) should not be used for diagnosis because they are associated with an increased risk of bacterial cholangitis.

The differential diagnosis should include primary sclerosing cholangitis, isolated polycystic liver disease, and hepatic cystic hamartoma (see these terms), as well as hepatic and choledochal cysts.

Cases of prenatal diagnosis based on ultrasonographic findings have been reported.

Most cases of CD are sporadic. Syndromic cases (CS) share with congenital hepatic fibrosis and recessive polycystic kidney disease an autosomal recessive transmission.

Management depends on the clinical presentation, localization and stage of the disease. Ursodeoxycholic acid may be used to prevent stone formation. Antibiotics are used for cholangitis. Radiological, endoscopic, and surgical intervention may be required for patients with biliary obstruction, abscess formation and liver or bile duct stones. Patients with severe disease may be candidates for liver transplantation.

Quality of life may be significantly affected by recurrent cholangitis. Prognosis depends on the clinical course and the risk of cholangiocarcinoma.