There is no way to reverse VHL mutations, but early recognition and treatment of specific manifestations of VHL can substantially decrease complications and improve quality of life. For this reason, individuals with VHL disease are usually screened routinely for retinal angiomas, CNS hemangioblastomas, clear-cell renal carcinomas and pheochromocytomas. CNS hemangioblastomas are usually surgically removed if they are symptomatic. Photocoagulation and cryotherapy are usually used for the treatment of symptomatic retinal angiomas, although anti-angiogenic treatments may also be an option. Renal tumours may be removed by a partial nephrectomy or other techniques such as radiofrequency ablation.

ACE inhibitors have been proposed as a novel treatment of neurofibromas. ACE inhibitors are currently used to treat hypertension and congestive heart failure, to avert remodeling and reinfarction after myocardial infarction, and to ameliorate diabetic nephropathy and other renal diseases. ACE inhibitors work by indirectly down regulating TGF-beta, which is a growth factor that has been shown to influence the development of tumors.

Surgical resection of the tumor is the treatment of first choice, either by open laparotomy or laparoscopy. Given the complexity of perioperative management, and the potential for catastrophic intra and postoperative complications, such surgery should be performed only at centers experienced in the management of this disorder. In addition to the surgical expertise that such centers can provide, they will also have the necessary endocrine and anesthesia resources. It may also be necessary to carry out adrenalectomy, a complete surgical removal of the affected adrenal gland(s).

Either surgical option requires prior treatment with the non-specific and irreversible alpha adrenoceptor blocker phenoxybenzamine or a short acting alpha antagonist (e.g. prazosin, terazosin, or doxazosin). Doing so permits the surgery to proceed while minimizing the likelihood of severe intraoperative hypertension (as might occur when the tumor is manipulated). Some authorities would recommend that a combined alpha/beta blocker such as labetalol also be given in order to slow the heart rate. Regardless, a nonselective beta-adrenergic receptor blocker such as propranolol must never be used in the presence of a pheochromocytoma. The mechanism for β-adrenoceptor blocker-associated adverse events is generally ascribed to inhibition of β2-adrenoceptor-mediated vasodilatation, leaving α1-adrenoceptor-mediated vasoconstrictor responses to catecholamines unopposed and, thus, severe and potentially refractory hypertension. However some clinical guidelines permit beta-1 blockade use together with alpha blockers during surgery for control of tachycardia.

The patient with pheochromocytoma is invariably volume depleted. In other words, the chronically elevated adrenergic state characteristic of an untreated pheochromocytoma leads to near-total inhibition of renin-angiotensin activity, resulting in excessive fluid loss in the urine and thus reduced blood volume. Hence, once the pheochromocytoma has been resected, thereby removing the major source of circulating catecholamines, a situation arises where there is both very low sympathetic activity and volume depletion. This can result in profound hypotension. Therefore, it is usually advised to "salt load" pheochromocytoma patients before their surgery. This may consist of simple interventions such as consumption of high salt food pre-operatively, direct salt replacement or through the administration of intravenous saline solution.

Once a plexiform neurofibroma has undergone malignant transformation, radiation and chemotherapy can be used as treatment. However, radiation is generally not used as a treatment for plexiform neurofibromas because of concerns that this could actually promote malignant transformation. There has even been a documented case of a Schwannoma being induced from a neurofibroma due to radiation therapy.

Surgical removal of tumors is an option, however the risks involved should be assessed first. With regard to OPG (optic pathway gliomas), the preferred treatment is chemotherapy. However, radiotherapy isn't recommended in children who present with this disorder. It is recommended that children diagnosed with NF1 at an early age have an examination each year, which allows any potential growths or changes related to the disorder to be monitored.

The only curative treatment is complete surgical excision of the tumor, which can be performed even in the case of invasion into large blood vessels, such as the renal vein or inferior vena cava. The 5-year survival rate after successful surgery is 50–60%, but unfortunately, a large percentage of patients are not surgical candidates. Radiation therapy and radiofrequency ablation may be used for palliation in patients who are not surgical candidates.

Chemotherapy regimens typically include the drug mitotane, an inhibitor of steroid synthesis which is toxic to cells of the adrenal cortex, as well as standard cytotoxic drugs. A retrospective analysis showed a survival benefit for mitotane in addition to surgery when compared to surgery alone.

The two most common regimens are cisplatin, doxorubicin, etoposide + mitotane and streptozotocin + mitotane. It is unknown which regimen is better. Researchers at Uppsala University Hospital initiated a collaboration between adrenocortical cancer specialists in Europe, USA and Australia, to conduct the first ever randomized controlled trial in adrenocortical cancer (FIRM-ACT study), comparing these two regimens.

Prophylactic mastectomy to reduce the risk of breast cancer is an option.

The definitive management is surgical removal of the insulinoma. This may involve removing part of the pancreas, as well (Whipple procedure and distal pancreatectomy).

Medications such as diazoxide and somatostatin can be used to block the release of insulin for patients who are not surgical candidates or who otherwise have inoperable tumors.

Streptozotocin is used in islet cell carcinomas which produce excessive insulin. Combination chemotherapy is used, either doxorubicin and streptozotocin, or fluorouracil and streptotozocin in patients where doxorubicin is contraindicated.

In metastasizing tumors with intrahepatic growth, hepatic arterial occlusion or embolization can be used.

Some benign tumors need no treatment; others may be removed if they cause problems such as seizures, discomfort or cosmetic concerns. Surgery is usually the most effective approach and is used to treat most benign tumors. In some case other treatments may be of use. Adenomas of the rectum may be treated with sclerotherapy, a treatment in which chemicals are used to shrink blood vessels in order to cut off the blood supply. Most benign tumors do not respond to chemotherapy or radiation therapy, although there are exceptions; benign intercranial tumors are sometimes treated with radiation therapy and chemotherapy under certain circumstances. Radiation can also be used to treat hemangiomas in the rectum. Benign skin tumors are usually surgically resected but other treatments such as cryotherapy, curettage, electrodesiccation, laser therapy, dermabrasion, chemical peels and topical medication are used.

Wide excision is the treatment of choice, although attempting to preserve hearing. Based on the anatomic site, it is difficult to completely remove, and so while there is a good prognosis, recurrences or persistence may be seen. There is no metastatic potential. Patients who succumb to the disease, usually do so because of other tumors within the von Hippel-Lindau complex rather than from this tumor.

Recommendations for individuals from families affected by the syndrome include:

- Avoidance of radiation therapy to reduce risk of secondary radiation induced malignancies,

- Children and adults undergo comprehensive annual physical examination,

- Women undergo age specific breast cancer monitoring beginning at age 25 years, and

- All patients should consult a physician promptly for evaluation of lingering symptoms and illnesses.

Treatment for neurofibrosarcoma is similar to that of other cancers.

Surgery is an option; the removal of the tumor along with surrounding tissue may be vital for the patient’s survival. For discrete, localized tumors, surgery is often followed by radiation therapy of the excised area to reduce the chance of recurrence.

For patients suffering from neurofibrosarcomas in an extremity, if the tumor is vascularized (has its own blood supply) and has many nerves going through it and/or around it, amputation of the extremity may be necessary. Some surgeons argue that amputation should be the procedure of choice when possible, due to the increased chance of a better quality of life. Otherwise, surgeons may opt for a limb-saving treatment, by removing less of the surrounding tissue or part of the bone, which is replaced by a metal rod or grafts.

Radiation will also be used in conjunction with surgery, especially if the limb was not amputated. Radiation is rarely used as a sole treatment.

In some instances, the oncologist may choose chemotherapy drugs when treating a patient with neurofibrosarcoma, usually in conjunction with surgery. Patients taking chemotherapy must be prepared for the side effects that come with any other chemotherapy treatment, such as; hair loss, lethargy, weakness, etc.

The different manifestations of Birt–Hogg–Dubé syndrome are controlled in different ways. The fibrofolliculomas can be removed surgically, through curettage, shave excision, skin resurfacing, or laser ablation; however, this is not a permanent solution as the tumors often recur. The renal and pulmonary symptoms are managed preventatively: CT scans, ultrasounds, or MRIs of the kidneys are recommended regularly, and family members are advised not to smoke. MRIs are the preferred method for surveillance of the kidneys in people with BHD because they do not carry the same risk of radiation complications as CT scans and are more sensitive than ultrasounds. Smokers with Birt–Hogg–Dubé have more severe pulmonary symptoms than non-smokers. Though nephrectomy is sometimes indicated, kidney tumors in cases of Birt–Hogg–Dubé are often removed without taking the whole kidney, in a procedure called partial nephrectomy. Knockout mouse studies have shown that administration of rapamycin may mitigate the effects of FLCN mutations on kidneys and improve renal cancer prognoses because of folliculin's interaction with the mTOR pathway.

In general, treatment for PanNET encompasses the same array of options as other neuroendocrine tumors, as discussed in that main article. However, there are some specific differences, which are discussed here.

In functioning PanNETs, octreotide is usually recommended prior to biopsy or surgery but is generally avoided in insulinomas to avoid profound hypoglycemia.

PanNETs in MEN1 are often multiple, and thus require different treatment and surveillance strategies.

Some PanNETs are more responsive to chemotherapy than are gastroenteric carcinoid tumors. Several agents have shown activity. In well differentiated PanNETs, chemotherapy is generally reserved for when there are no other treatment options. Combinations of several medicines have been used, such as doxorubicin with streptozocin and fluorouracil (5-FU) and capecitabine with temozolomide. Although marginally effective in well-differentiated PETs, cisplatin with etoposide has some activity in poorly differentiated neuroendocrine cancers (PDNECs), particularly if the PDNEC has an extremely high Ki-67 score of over 50%.

Several targeted therapy agents have been approved in PanNETs by the FDA based on improved progression-free survival (PFS):

- everolimus (Afinitor) is labeled for treatment of progressive neuroendocrine tumors of pancreatic origin in patients with unresectable, locally advanced or metastatic disease. The safety and effectiveness of everolimus in carcinoid tumors have not been established.

- sunitinib (Sutent) is labeled for treatment of progressive, well-differentiated pancreatic neuroendocrine tumors in patients with unresectable locally advanced or metastatic disease. Sutent also has approval from the European Commission for the treatment of 'unresectable or metastatic, well-differentiated pancreatic neuroendocrine tumors with disease progression in adults'. A phase III study of sunitinib treatment in well differentiated pNET that had worsened within the past 12 months (either advanced or metastatic disease) showed that sunitinib treatment improved progression-free survival (11.4 months vs. 5.5 months), overall survival, and the objective response rate (9.3% vs. 0.0%) when compared with placebo.

There is increased life-time risk of secondary cancers (relative risk 3.63), with a slightly increased mortality risk (1.21) according to a 2004 Swedish study of 481 patients.

Resection of the polyps is required only if serious bleeding or intussusception occurs. Enterotomy is performed for removing large, single nodules. Short lengths of heavily involved intestinal segments can be resected. Colonoscopy can be used to snare the polyps if they are within reach.

Treatment is usually supportive treatment, that is, treatment to reduce any symptoms rather than to cure the condition.

- Enucleation of the odontogenic cysts can help, but new lesions, infections and jaw deformity are usually a result.

- The severity of the basal-cell carcinoma determines the prognosis for most patients. BCCs rarely cause gross disfigurement, disability or death .

- Genetic counseling

A recommend surveillance program for Multiple Endocrine Neoplasia Type 1 has been suggested by the International Guidelines for Diagnosis and Therapy of MEN syndromes group.

Chemotherapy is often used as part of treatment. Evidence of benefit, however, is not clear as of 2013. A few different chemotherapeutic regimens for medulloblastoma are used, but most involve a combination of lomustine, cisplatin, carboplatin, vincristine, or cyclophosphamide. In younger patients (less than 3–4 years of age), chemotherapy can delay, or in some cases possibly even eliminate, the need for radiotherapy. However, both chemotherapy and radiotherapy often have long-term toxicity effects, including delays in physical and cognitive development, higher risk of second cancers, and increased cardiac disease risks.

Treatment begins with maximal surgical removal of the tumor. The addition of radiation to the entire neuraxis and chemotherapy may increase the disease-free survival. Some evidence indicates that proton beam irradiation reduces the impact of radiation on the cochlear and cardiovascular areas and reduces the cognitive late effects of cranial irradiation.

This combination may permit a 5-year survival in more than 80% of cases. The presence of desmoplastic features such as connective tissue formation offers a better prognosis. Prognosis is worse if the child is less than 3 years old, degree of resection is an inadequate , or if any CSF, spinal, supratentorial, or systemic spread occurs. Dementia after radiotherapy and chemotherapy is a common outcome appearing two to four years following treatment. Side effects from radiation treatment can include cognitive impairment, psychiatric illness, bone growth retardation, hearing loss, and endocrine disruption. Increased intracranial pressure may be controlled with corticosteroids or a ventriculoperitoneal shunt.

Surgery remains the front-line therapy for HNPCC. There is an ongoing controversy over the benefit of 5-fluorouracil-based adjuvant therapies for HNPCC-related colorectal tumours, particularly those in stages I and II.

Most patients with benign insulinomas can be cured with surgery. Persistent or recurrent hypoglycemia after surgery tends to occur in patients with multiple tumors. About 2% of patients develop diabetes mellitus after their surgery.

The priority of retinoblastoma treatment is to preserve the life of the child, then to preserve vision, and then to minimize complications or side effects of treatment. The exact course of treatment will depend on the individual case and will be decided by the ophthalmologist in discussion with the paediatric oncologist. Children with involvement of both eyes at diagnosis usually require multimodality therapy (chemotherapy, local therapies)

The various treatment modalities for retinoblastoma includes:

- Enucleation of the eye – Most patients with unilateral disease present with advanced intraocular disease and therefore usually undergo enucleation, which results in a cure rate of 95%. In bilateral Rb, enucleation is usually reserved for eyes that have failed all known effective therapies or without useful vision.

- External beam radiotherapy (EBR) – The most common indication for EBR is for the eye in a young child with bilateral retinoblastoma who has active or recurrent disease after completion of chemotherapy and local therapies. However, patients with hereditary disease who received EBR therapy are reported to have a 35% risk of second cancers.

- Brachytherapy – Brachytherapy involves the placement of a radioactive implant (plaque), usually on the sclera adjacent to the base of a tumor. It used as the primary treatment or, more frequently, in patients with small tumors or in those who had failed initial therapy including previous EBR therapy.

- Thermotherapy – Thermotherapy involves the application of heat directly to the tumor, usually in the form of infrared radiation. It is also used for small tumors

- Laser photocoagulation – Laser photocoagulation is recommended only for small posterior tumors. An argon or diode laser or a xenon arc is used to coagulate all the blood supply to the tumor.

- Cryotherapy – Cryotherapy induces damage to the vascular endothelium with secondary thrombosis and infarction of the tumor tissue by rapidly freezing it. Cryotherapy may be used as primary therapy for small peripheral tumors or for small recurrent tumors previously treated with other methods.

- Systemic chemotherapy – Systemic chemotherapy has become forefront of treatment in the past decade, in the search of globe preserving measures and to avoid the adverse effects of EBR therapy. The common indications for chemotherapy for intraocular retinoblastoma include tumors that are large and that cannot be treated with local therapies alone in children with bilateral tumors. It is also used in patients with unilateral disease when the tumors are small but cannot be controlled with local therapies alone.

- Intra-arterial chemotherapy – Chemotherapeutic drugs are administered locally via a thin catheter threaded through the groin, through the aorta and the neck, directly into the optic vessels.

- Nano-particulate chemotherapy – To reduce the adverse effects of systemic therapy, subconjuctival (local) injection of nanoparticle carriers containing chemotherapeutic agents (carboplatin) has been developed which has shown promising results in the treatment of retinoblastoma in animal models without adverse effects.

- Chemoreduction - A combined approach using chemotherapy to initially reduce the size of the tumor, and adjuvant focal treatments, such as transpupillary thermotherapy, to control the tumor.

Chemotherapy regimens for pediatric ependymomas have produced only modest benefit and degree of resection remains the most conspicuous factor in recurrence and survival.

The association of "TERT" expression with poor outcome in pediatric ependymomas has driven some researchers to suggest that telomerase inhibition may be an effective adjuvant therapy for pediatric ependymomas. Further, data from "in vitro" experiments using primary tumor isolate cells suggest that inhibition of telomerase activity may inhibit cell proliferation and increase sensitivity of cells to DNA damaging agents, consistent with the observation of high telomerase activity in primary tumors. Additionally, because apurinic/apyrimidinic endonuclease ("APE1") has been found to confer radiation resistance in pediatric ependymomas, it has been suggested that inhibitors of Ap endo activity might also restore radiation sensitivity.

Within the infratentorial group of pediatric ependymomas, radiotherapy was found to significantly increase 5-year survival. However, a retrospective review of sterotactic radiosurgery showed it provided only a modest benefit to patients who had previously undergone resection and radiation. Though other supratentorial tumors tend to have a better prognosis, supratentorial anaplastic ependymomas are the most aggressive ependymoma and neither total excision nor postoperative irradiation was found to be effective in preventing early recurrence.

Following resection of infratentorial ependymomas, residual tumor is more likely in lateral versus medial tumors, classified radiologically pre-operatively. Specific techniques, such as cerebellomedullary fissure dissection have been proposed to aid in complete resection while avoiding iatrogenic effects in these cases. Surveillance neuroimaging for recurrence provides additional survival to patients over observation alone.

Children with cerebellar pilocytic astrocytoma may experience side effects related to the tumor itself depending on the location and related to the treatment. Strabismus.

- Symptoms related to increased pressure in the brain often disappear after surgical removal of the tumor.

- Effects on coordination and balance improved and might progressively (to completely) disappear as recovery progresses.

- Steroid-treatment is often used to control tissue swelling that may occur pre- and post-operatively.

- Children Diagnosed can also suffer long term side effects due to the type of treatment they may receive.