The treatment options for autosomal recessive polycystic kidney disease, given there is no current cure, are:

- Medications for hypertension

- Medications and/or surgery for pain

- Antibiotics for infection

- Kidney transplantation(in serious cases)

- Dialysis (if renal failure)

There is no FDA-approved treatment. However, it has been shown that mild to moderate dietary restrictions slow the progression of autosomal dominant polycystic kidney disease (ADPKD).

If and when the disease progresses enough in a given case, the nephrologist or other practitioner and the patient will have to decide what form of renal replacement therapy will be used to treat end-stage kidney disease (kidney failure, typically stage 4 or 5 of chronic kidney disease).

That will either be some form of dialysis, which can be done at least two different ways at varying frequencies and durations (whether it is done at home or in the clinic depends on the method used and the patient's stability and training) and eventually, if they are eligible because of the nature and severity of their condition and if a suitable match can be found, unilateral or bilateral kidney transplantation.

A Cochrane Review study of autosomal dominant polycystic kidney disease made note of the fact that it is important at all times, while avoiding antibiotic resistance, to control infections of the cysts in the kidneys, and if affected, the liver, when needed for a certain duration to combat infection, by using, quote: "bacteriostatic and bacteriocidal drugs".

ADPKD individuals might have a normal life; conversely, ARPKD can cause kidney dysfunction and can lead to kidney failure by the age of 40-60. ADPKD1 and ADPKD2 are very different, in that ADPKD2 is much milder.

Currently, there are no therapies proven effective to prevent the progression of polycystic kidney disease (autosomal dominant).

Autosomal recessive polycystic kidney disease (ARPKD) is the recessive form of polycystic kidney disease. It is associated with a group of congenital fibrocystic syndromes. Mutations in the "PKHD1" (chromosomal locus 6p12.2) cause ARPKD.

Many forms of cystic kidney disease can be detected in children prior to birth. Abnormalities which only affect one kidney are unlikely to cause a problem with the healthy arrival of a baby. Abnormalities which affect both kidneys can have an effect on the baby's amniotic fluid volume which can in turn lead to problems with lung development. Some forms of obstruction can be very hard to differentiate from cystic renal disease on early scans.

Cystic kidney disease refers to a wide range of hereditary, developmental, and acquired conditions. With the inclusion of neoplasms with cystic changes, over 40 classifications and subtypes have been identified. Depending on the disease classification, the presentation of disease may be from birth, or much later into adult life. Cystic disease may involve one or both kidneys and may or may not occur in the presence of other anomalies. A higher incidence of cystic kidney disease is found in the male population and prevalence increases with age. Renal cysts have been reported in more than 50% of patients over the age of 50. Typically, cysts grow up to 2.88 mm annually and cause related pain and/or hemorrhage.

Of the cystic kidney diseases, the most common is Polycystic kidney disease; having two prevalent sub-types: autosomal recessive and autosomal dominant polycystic kidney disease. Autosomal Recessive Polycystic Kidney Disease (ARPKD) is primarily diagnosed in infants and young children. Autosomal dominant polycystic kidney disease (ADPKD) is most often diagnosed in adulthood.

Another example of cystic kidney disease is Medullary sponge kidney.

The treatment depends on clinical features and the location of the biliary abnormality. When the disease is localized to one hepatic lobe, hepatectomy relieves symptoms and appears to remove the risk of malignancy. Good evidence suggests that malignancy complicates Caroli disease in roughly 7% of cases.

Antibiotics are used to treat the inflammation of the bile duct, and ursodeoxycholic acid is used for hepatolithiasis. Ursodiol is given to treat cholelithiasis. In diffuse cases of Caroli disease, treatment options include conservative or endoscopic therapy, internal biliary bypass procedures, and liver transplantation in carefully selected cases. Surgical resection has been used successfully in patients with monolobar disease. An orthotopic liver transplant is another option, used only when antibiotics have no effect, in combination with recurring cholangitis. With a liver transplant, cholangiocarcinoma is usually avoided in the long run.

Family studies are necessary to determine if Caroli disease is due to inheritable causes. Regular follow-ups, including ultrasounds and liver biopsies, are performed.

Mortality is indirect and caused by complications. After cholangitis occurs, patients typically die within 5–10 years.