For simple cases of cystic echinococcosis, the most common form of treatment is open surgical removal of the cysts combined with chemotherapy using albendazole and/or mebendazole before and after surgery. However, if there are cysts in multiple organs or tissues, or the cysts are in risky locations, surgery becomes impractical. For inoperable cases such as these, chemotherapy and/or PAIR (puncture-aspiration-injection-reaspiration) become alternative options of treatment. In the case of alternative treatment using just chemotherapy, albendazole is preferred twice a day for 1–5 months. An alternative to albendazole is mebendazole for at least 3 to 6 months. The other alternative to surgery is PAIR with chemotherapy. PAIR is a minimally invasive procedure that involves three steps: puncture and needle aspiration of the cyst, injection of a scolicidal solution for 20–30 min, and cyst-re-aspiration and final irrigation. Patients who undergo PAIR typically take albendazole or mebendazole from 7 days before the procedure until 28 days after the procedure. While open surgery still remains as the standard for cystic echinococcosis treatment, there have been a number of studies that suggest that PAIR with chemotherapy is more effective than surgery in terms of disease recurrence, and morbidity and mortality. In addition to the three above mentioned treatments, there is currently research and studies looking at new treatment involving percutaneous thermal ablation (PTA) of the germinal layer in the cyst by means of a radiofrequency ablation device. This form of treatment is still relatively new and requires much more testing before being widely used. An alternative to open surgery is laparoscopic surgery, which provides excellent cure rates with minimal morbidity and mortality.

For alveolar echinococcosis, surgical removal of cysts combined with chemotherapy (using albendazole and/or mebendazole) for up to two years after surgery is the only sure way to completely cure the disease. However, in inoperable cases, chemotherapy by itself can also be used. In treatment using just chemotherapy, one could use either mebendazole in three doses or albendazole in two doses. Since chemotherapy on its own is not guaranteed to completely rid the patient of disease, patients are often kept on the drugs for extended periods of times (i.e. more than 6 months, years). In addition to surgery and chemotherapy, liver transplants are being looked into as a form of treatment for alveolar echinococcosis although it is seen as incredibly risky since it often leads to echinococcosis re-infection in the patient afterwards.

Tapeworms are treated with medications taken by mouth, usually in a single dose. The drug of choice for tapeworm infections is praziquantel. Niclosamide can also be used.

Alveolar hydatid disease (AHD), also known as alveolar echinococcosis, alveolar colloid of the liver, alveolococcosis, multilocular echinococcosis, and small fox tapeworm is a form of echinococcosis, and is a disease that originates from a parasite. Although alveolar echinococcosis is rarely diagnosed in humans and is not as widespread as cystic echinococcosis, it is also still a serious disease that not only has a significantly high fatality rate but also has the potential to become an emerging disease in many countries.

Most occurrences are found in areas that lack adequate sanitation and include Southeast Asia, West Africa, and East Africa.

Currently, the only clinical/pharmacological treatment available for ADPKD consists in reducing the speed in gain of total kidney volume (TKV) with aquaretics (i.e. tolvaptan), which can alleviate pain while giving the patients a better quality of life for over a mean of 3 years. After this period, patients can restart gaining TKV at pre-treatment rates and may eventually have to go through dialysis and kidney transplant. Paliative treatment modalities involve symptomatic medications (non-opioid and opioid analgesics) for abdominal/retroperitoneal pain. Before the advent of aquaretic medication, the only option for analgesic-resistant pain were simple or complex surgical procedures (i.e. renal cyst aspiration, cyst decortication, renal denervation and nephrectomy), which can result in complications inherent to surgery.

In 2014, Japan was the first country in the world to approve a pharmacological treatment for ADPKD followed by Canada and Europe, which approved the drug tolvaptan for ADPKD patients in the beginning of 2015. Tolvaptan, an aquaretic drug, is a vasopressin receptor 2 (V2) antagonist. Pre-clinical studies had suggested that the molecule cAMP could be involved in the enlargement of ADPKD cysts, and studies on rodents confirmed the role of vasopressin in increasing the levels of cAMP in the kidney, which laid the basis for the conduction of clinical studies. Because data from the Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease (CRISP) led by Mayo Clinic showed that total kidney volume (TKV) predicted the risk of developing renal insufficiency in patients with ADPKD, the TEMPO 3:4 trial, which enrolled patients from 129 sites worldwide from 2007 to 2009, evaluated TKV as a primary end-point to test the efficacy of tolvaptan in ADPKD patients. That study showed a significant decrease in the ratio of TKV increase and deterring of renal function decline in ADPKD patients after treatment with tolvaptan; however, because laboratory test results regarding liver function appeared elevated in a percentage of patients enrolled in that study, the approval of the drug was either delayed by regulatory agencies or, as in case of the US, altogether denied.

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".

The management of this condition can be done via-improvement of any electrolyte imbalance, as well as, hypertension and anemia treatment as the individuals condition warrants.

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).

This system is more directly focused on the most appropriate management. These alternatives are broadly to ignore the cyst, schedule follow-up or perform a surgical excision of it. When a cyst shows discrepancy in severity across categories, it is the most worrisome feature that is used in deciding about management. There is no established rule regarding the follow-up frequency, but one possibility is after 6 months, which can later be doubled if unchanged.

The uterine curettage is generally done under the effect of anesthesia, preferably spinal anesthesia in hemodynamically stable patients. The advantages of spinal anesthesia over general anesthesia include ease of technique, favorable effects on the pulmonary system, safety in patients with hyperthyroidism and non-tocolytic pharmacological properties. Additionally, by maintaining patient’s consciousness one can diagnose the complications like uterine perforation, cardiopulmonary distress and thyroid storm at an earlier stage than when the patient is sedated or is under general anesthesia.

Hydatidiform moles should be treated by evacuating the uterus by uterine suction or by surgical curettage as soon as possible after diagnosis, in order to avoid the risks of choriocarcinoma. Patients are followed up until their serum human chorionic gonadotrophin (hCG) level has fallen to an undetectable level. Invasive or metastatic moles (cancer) may require chemotherapy and often respond well to methotrexate. As they contain paternal antigens, the response to treatment is nearly 100%. Patients are advised not to conceive for half a year after hCG levels have normalized. The chances of having another molar pregnancy are approximately 1%.

Management is more complicated when the mole occurs together with one or more normal fetuses.

Pain associated with ovarian cysts may be treated in several ways:

- Pain relievers such as acetaminophen, nonsteroidal anti-inflammatory drugs, or opioids.

- While hormonal birth control prevents the development of new cysts in those who frequently get them, it is not useful for the treatment of current cysts.

The complex cyst can be further evaluated with doppler ultrasonography, and for Bosniak classification and follow-up of complex cysts, either contrast-enhanced ultrasound (CEUS) or contrast CT is used.

The cysts can be removed via , though conventional cyst excision techniques have proven impractical, and a specialized regimen is required.

Medications for PCOS include oral contraceptives and metformin. The oral contraceptives increase sex hormone binding globulin production, which increases binding of free testosterone. This reduces the symptoms of hirsutism caused by high testosterone and regulates return to normal menstrual periods. Metformin is a drug commonly used in type 2 diabetes to reduce insulin resistance, and is used off label (in the UK, US, AU and EU) to treat insulin resistance seen in PCOS. In many cases, metformin also supports ovarian function and return to normal ovulation. Spironolactone can be used for its antiandrogenic effects, and the topical cream eflornithine can be used to reduce facial hair. A newer insulin resistance drug class, the thiazolidinediones (glitazones), have shown equivalent efficacy to metformin, but metformin has a more favorable side effect profile. The United Kingdom's National Institute for Health and Clinical Excellence recommended in 2004 that women with PCOS and a body mass index above 25 be given metformin when other therapy has failed to produce results. Metformin may not be effective in every type of PCOS, and therefore there is some disagreement about whether it should be used as a general first line therapy. The use of statins in the management of underlying metabolic syndrome remains unclear.

It can be difficult to become pregnant with PCOS because it causes irregular ovulation. Medications to induce fertility when trying to conceive include the ovulation inducer clomiphene or pulsatile leuprolide. Metformin improves the efficacy of fertility treatment when used in combination with clomiphene. Metformin is thought to be safe to use during pregnancy (pregnancy category B in the US). A review in 2014 concluded that the use of metformin does not increase the risk of major birth defects in women treated with metformin during the first trimester.

TSC typically affects multiple organ systems and manifests differently in each patient and in different stages of the life course. Drug therapy, surgery, and other interventions can be effective in managing some of the manifestations and symptoms of TSC.

In the United States, the Food and Drug Administration has approved several drugs for managing some of the major manifestations of TSC. The antiepileptic medication vigabatrin was approved in 2009 for treatment of infantile spasms and was recommended as first-line therapy for infantile spasms in children with TSC by the 2012 International TSC Consensus Conference. Adrenocorticotropic hormone was approved in 2010 to treat infantile spasms. Everolimus was approved for treatment of TSC-related tumors in the brain (subependymal giant cell astrocytoma) in 2010 and in the kidneys (renal angiomyolipoma) in 2012. Everolimus also showed evidence of effectiveness at treating epilepsy in some people with TSC. In 2017, the European Commission approved everolimus for treatment of refractory partial-onset seizures associated with TSC.

Neurosurgical intervention may reduce the severity and frequency of seizures in TSC patients. Embolization and other surgical interventions can be used to treat renal angiomyolipoma with acute hemorrhage. Surgical treatments for symptoms of lymphangioleiomyomatosis (LAM) in adult TSC patients include pleurodesis to prevent pneumothorax and lung transplantation in the case of irreversible lung failure.

Other treatments that have been used to treat TSC manifestations and symptoms include a ketogenic diet for intractable epilepsy and pulmonary rehabilitation for LAM.

Orofaciodigital syndrome type 1 can be treated with reconstructive surgery or the affected parts of the body. Surgery of cleft palate, tongue nodules, additional teeth, accessory frenulae, and orthodontia for malocclusion. Routine treatment for patients with renal disease and seizures may also be necessary. Speech therapy and special education in the later development may also be used as management.

Although most cases of ovarian cysts involve monitoring, some cases require surgery. This may involve removing the cyst, or one or both ovaries. Technique is typically laparoscopic, unless the cyst is particularly large, or if pre-operative imaging suggests malignancy or complex anatomy. In certain situations, the cyst is entirely removed, while with cysts with low recurrence risk, younger patients, or which are in anatomically eloquent areas of the pelvis, they can be drained. Features that may indicate the need for surgery include:

- Persistent complex ovarian cysts

- Persistent cysts that are causing symptoms

- Complex ovarian cysts larger than 5 cm

- Simple ovarian cysts larger 10 cm or larger than 5 cm in postmenopausal patients

- Women who are menopausal or perimenopausal

A 2017 review concluded that while both myo-inositol and D-chiro-inositols may regulate menstrual cycles and improve ovulation, there is a lack of evidence regarding effects on the probability of pregnancy. A 2012 and 2017 review have found myo-inositol supplementation appears to be effective in improving several of the hormonal disturbances of PCOS. A 2011 review found not enough evidence to conclude any beneficial effect from D-chiro-inositol. There is insufficient evidence to support the use of acupuncture.

There is no causative / curative therapy. Symptomatic medical treatments are focussing on symptoms caused by orthopaedic, dental or cardiac problems. Regarding perioperative / anesthesiological management, recommendations for medical professionals are published at OrphanAnesthesia.

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.

Polycystic liver disease (PLD) usually describes the presence of multiple cysts scattered throughout normal liver tissue, in association with polycystic kidney disease.