The goal of treatment is to improve the appearance of lesions since they are otherwise not serious and typically do not cause symptoms. Many treatment methods have been attempted however, complete removal is uncommon. No single treatment method has been shown to consistently work. Both medical and surgical treatments have been studied, each with variable success. Common destructive treatment methods include carbon dioxide lasers, dermabrasion, surgical excision, electrocoagulation and chemical peels. Many of these methods are very time consuming and require multiple treatment sessions.Carbon dioxide lasers are the most commonly practiced method; however, can cause thermal damage leading to scarring in the area. Medical therapies include topical atropine, topical retinoids and oral tranilast.

The most common adverse side effects include redness, skin discoloration and pain. Other side effects include blistering and scarring.

Treatment for cystic hygroma involves the removal of the abnormal tissue; however complete removal may be impossible without removing other normal areas. Surgical removal of the tumor is the typical treatment provided, with the understanding that additional removal procedures will most likely be required as the lymphangioma grows. Most patients need at least two procedures done for the removal process to be achieved. Recurrence is possible but unlikely for those lesions able to be removed completely via excisional surgery. Radiotherapy and chemical cauteries are not as effective with the lymphangioma than they are with the hemangioma. Draining lymphangiomas of fluid provides only temporary relief, so they are removed surgically. Cystic Hygroma can be treated with OK432 (Picibanil).

The least invasive and most effective form of treatment is now performed by interventional radiologists. A sclerosing agent, such as 1% or 3% sodium tetradecyl sulfate, doxycycline, or ethanol, may be directly injected into a lymphocele. "All sclerosing agents are thought to work by ablating the endothelial cells of the disrupted lymphatics feeding into the lymphocele."

Lymphangioma circumscription can be healed when treated with a flashlamp pulsed dye laser, although this can cause port-wine stains and other vascular lesions.

As the causes of local gigantism are varied, treatment depends on the particular condition. Treatment may range from antibiotics and other medical therapy, to surgery in order to correct the anatomical anomaly.

Most of these tumors are treated with surgical removal. It is non recurrent.

A baby with a prenatally diagnosed cystic hygroma should be delivered in a major medical center equipped to deal with neonatal complications, such as a neonatal intensive care unit. An obstetrician usually decides the method of delivery. If the cystic hygroma is large, a cesarean section may be performed. After birth, infants with a persistent cystic hygroma must be monitored for airway obstruction. A thin needle may be used to reduce the volume of the cystic hygroma to prevent facial deformities and airway obstruction. Close observation of the baby by a neonatologist after birth is recommended. If resolution of the cystic hygroma does not occur before birth, a pediatric surgeon should be consulted.

Cystic hygromas that develop in the third trimester, after thirty weeks gestation, or in the postnatal period are usually not associated with chromosome abnormalities. There is a chance of recurrence after surgical removal of the cystic hygroma. The chance of recurrence depends on the extent of the cystic hygroma and whether its wall was able to be completely removed.

Treatments for removal of cystic hygroma are surgery or sclerosing agents which include:

- Bleomycin

- Doxycycline

- Ethanol (pure)

- Picibanil (OK-432)

- Sodium tetradecyl sulfate

As Becker's nevus is considered a benign lesion, treatment is generally not necessary except for cosmetic purposes. Shaving or trimming can be effective in removing unwanted hair, while electrology or laser hair removal may offer a longer-lasting solution. Different types of laser treatments may also be effective in elimination or reduction of hyperpigmentation, though the results of laser treatments for both hair and pigment reduction appear to be highly variable.

People with juvenile polyps may require yearly upper and lower endoscopies with polyp excision and cytology. Their siblings may also need to be screened regularly. Malignant transformation of polyps requires surgical colectomy.

In terms of treatment/management one should observe what signs or symptoms are present and therefore treat those as there is no other current guideline. The affected individual should be monitored for cancer of:

- Thyroid

- Breast

- Renal

Treatment is not needed in the asymptomatic patient. Symptomatic patients may benefit from surgical debulking of the tumor. Complete tumor removal is not usually needed and can be difficult due to the tumor location.

These lesions rarely require surgery unless they are symptomatic or the diagnosis is in question. Since these lesions do not have malignant potential, long-term observation is unnecessary. Surgery can include the removal of the head of the pancreas (a pancreaticoduodenectomy), removal of the body and tail of the pancreas (a distal pancreatectomy), or rarely removal of the entire pancreas (a total pancreatectomy). In selected cases the surgery can be performed using minimally invasive techniques such as laparoscopy.

Wide, radical, complete surgical excision is the treatment of choice, with free surgical margins to achieve the best outcome and lowest chance of recurrence. Radiation is only used for palliation. In general, there is a good prognosis, although approximately 50% of patients die from disease within 3–10 years of presentation.

The prognosis for lymphangioma circumscriptum and cavernous lymphangioma is generally excellent. This condition is associated with minor bleeding, recurrent cellulitis, and lymph fluid leakage. Two cases of lymphangiosarcoma arising from lymphangioma circumscriptum have been reported; however, in both of the patients, the preexisting lesion was exposed to extensive radiation therapy.

In cystic hygroma, large cysts can cause dysphagia, respiratory problems, and serious infection if they involve the neck. Patients with cystic hygroma should receive cytogenetic analysis to determine if they have chromosomal abnormalities, and parents should receive genetic counseling because this condition can recur in subsequent pregnancies.

Complications after surgical removal of cystic hygroma include damage to the structures in the neck, infection, and return of the cystic hygroma.

Hormonal suppressive therapy with luteinizing hormone receptor agonists like leuprolide can be used to treat the seizure component, and are effective in most patients.

Surgery is offered if there is failure of medical therapy or rapid growth of lesion, with specific options including stereotactic thermocoagulation, gamma knife radiosurgery, and physical resection by transsphenoidal microsurgery. Surgical response is typically better when the seizure focus has been found by EEG to originate in or near the mass. The specific location of the lesion relative to the pituitary and infundibulum and the amount of hormonal disturbance at presentation can help predict risk of hypopituitarism following surgery.

Small chorangiomas are not treated. Large chorangioma can be treated several ways, including chemical ablation and laser coagulation.

Many people with CF are on one or more antibiotics at all times, even when healthy, to prophylactically suppress infection. Antibiotics are absolutely necessary whenever pneumonia is suspected or a noticeable decline in lung function is seen, and are usually chosen based on the results of a sputum analysis and the person's past response. This prolonged therapy often necessitates hospitalization and insertion of a more permanent IV such as a peripherally inserted central catheter or Port-a-Cath. Inhaled therapy with antibiotics such as tobramycin, colistin, and aztreonam is often given for months at a time to improve lung function by impeding the growth of colonized bacteria. Inhaled antibiotic therapy helps lung function by fighting infection, but also has significant drawbacks such as development of antibiotic resistance, tinnitus, and changes in the voice. Inhaled levofloxacin may be used to treat "Pseudomonas aeruginosa" in people with cystic fibrosis who are infected.

Antibiotics by mouth such as ciprofloxacin or azithromycin are given to help prevent infection or to control ongoing infection. The aminoglycoside antibiotics (e.g. tobramycin) used can cause hearing loss, damage to the balance system in the inner ear or kidney failure with long-term use. To prevent these side-effects, the amount of antibiotics in the blood is routinely measured and adjusted accordingly.

Several mechanical techniques are used to dislodge sputum and encourage its expectoration. In the hospital setting, chest physiotherapy is used; a respiratory therapist percusses an individual's chest by hand several times a day, to loosen up secretions. Chest physiotherapy is beneficial for short-term airway clearance. Devices that recreate this percussive therapy include the ThAIRapy Vest and the intrapulmonary percussive ventilator. Other methods such as biphasic cuirass ventilation, and associated clearance mode available in such devices, integrate a cough assistance phase, as well as a vibration phase for dislodging secretions. These are portable and adapted for home use.

Ivacaftor is a medication taken by mouth for the treatment of CF due to a number of specific mutations. It improves lung function by about 10%; however, as of 2014 it is expensive.

Aerosolized medications that help loosen secretions include dornase alfa and hypertonic saline. Dornase is a recombinant human deoxyribonuclease, which breaks down DNA in the sputum, thus decreasing its viscosity. Denufosol, an investigational drug, opens an alternative chloride channel, helping to liquefy mucus. Whether inhaled corticosteroids are useful is unclear, but stopping inhaled corticosteroid therapy is safe. There is weak evidence that corticosteroid treatment may cause harm by interfering with growth.

As lung disease worsens, mechanical breathing support may become necessary. Individuals with CF may need to wear special masks at night to help push air into their lungs. These machines, known as bilevel positive airway pressure (BiPAP) ventilators, help prevent low blood oxygen levels during sleep. Non-invasive ventilators may be used during physical therapy to improve sputum clearance. It is not known if this type of therapy has an impact on pulmonary exacerbations or disease progression. It is not known what role non-invasive ventilation therapy has for improving exercise capacity in people with cystic fibrosis. During severe illness, a tube may be placed in the throat (a procedure known as a tracheostomy) to enable breathing supported by a ventilator.

For children, preliminary studies show massage therapy may help people and their families' quality of life. Pneumococcal vaccination has not been studied as of 2014.

Some lung infections require surgical removal of the infected part of the lung. If this is necessary many times, lung function is severely reduced.

A folliculosebaceous-apocrine hamartoma, also known as "follicular-apocrine hamartoma", is a benign proliferation of the folliculosebaceous-apocrine unit.

A basaloid follicular hamartoma is a cutaneous condition characterized as distinctive benign adnexal tumor that has several described variants.

Folliculosebaceous cystic hamartoma abbreviated as (FSCH) is a rare cutaneous hamartoma consisting of dilated folliculosebaceous units invested in mesenchymal elements. it typically affects adults, have a predilection for the central face or scalp, with less than 1.5 cm dimension. Clinically, the lesions are asymptomatic, rubbery to firm in consistency, and usually occur on or above the neck in (> 90%) of cases, Histopathologically, FSCH shares several similar features to sebaceous trichofolliculoma, but it is usually possible to differentiate these two tumors.

While there is no cure for JBS, treatment and management of specific symptoms and features of the disorder are applied and can often be successful. Variability in the severity of JBS on a case-by-case basis determines the requirements and effectiveness of any treatment selected.

Pancreatic insufficiency and malabsorption can be managed with pancreatic enzyme replacement therapy, such as pancrelipase supplementation and other related methods.

Craniofacial and skeletal deformities may require surgical correction, using techniques including bone grafts and osteotomy procedures. Sensorineural hearing loss can be managed with the use of hearing aids and educational services designated for the hearing impaired.

Special education, specialized counseling methods and occupational therapy designed for those with mental retardation have proven to be effective, for both the patient and their families. This, too, is carefully considered for JBS patients.

Based on a survey of >800, surgical removal of the entire involved kidney plus the peri-renal fat appeared curative for the majority of all types of mesoblastic nephroma; the patient overall survival rate was 94%. Of the 4% of non-survivors, half were due to surgical or chemotherapeutic treatments. Another 4% of these patients suffered relapses, primarily in the local area of surgery rare cases of relapse due to lung or bone metastasis.. About 60% of these recurrent cases had a complete remission following further treatment. Recurrent disease was treated with a second surgery, radiation, and/or chemotherapy that often vincristine and actinomycin treatment. Removal of the entire afflicted kidney plus the peri-renal fat appears critical to avoiding local recurrences. In general, patients who were older than 3 months of age at diagnosis or had the cellular form of the disease, stage III disease, or involvement of renal lymph nodes had a higher recurrence rate. Among patients with these risk factors, only those with lymph node involvement are recommended for further therapy.

It has been suggested that mesoblastic nephroma patients with lymph node involvement or recurrent disease might benefit by adding the ALK inhibitor, crizotinib, or a tyrosine kinase inhibitor, either larotrectinib or entrectinib, to surgical, radiation, and/or chemotherapy treatment regimens. These drugs inhibit NTRK3's tyrosine kinase activity. Crizotinib has proven useful in treating certain cases of acute lymphoblastic leukemia that are associated with the "ETV6-NTRK3" fusion gene while larotrectinib and entrectinib have been useful in treating various cancers (e.g. a metastatic sarcoma, papillary thyroid cancer, non-small-cell lung carcinoma, gastrointestinal stromal tumor, mammary analog secretory carcinoma, and colorectal cancer) that are driven by mutated, overly active tyrosine kinases. Relevant to this issue, a 16-month-old girl with infantile fibrosarcoma harboring the "ETV6–NTRK3" fusion gene was successfully trated with larotrectinib. The success of these drugs, howwever, will likely depend on the relative malignancy-promoting roles of ETV6-NTRK3 protein's tyrosine kinase activity, the lose of ETV6-related transcription activity accompanying formation of ETV6-NTRK3 protein, and the various trisomy chromosomes that populate mesoblastic nephroma.

Patients are usually managed by a multidisciplinary team including surgeons, gynecologists, and dermatologists because of the complex nature of this disorder. Follow-up for the increased risk of breast cancer risk includes monthly breast self-examination, annual breast examination, and mammography at age 30 or five years earlier than the youngest age of breast cancer in the family. The magnitude of the risk of breast cancer justifies routine screening with breast MRI as per published guidelines.

Mucinous nevus (also known as "Nevus mucinosus") is a rare cutaneous condition characterized by hamartoma that can be congenital or acquired.

In most cases, a fetus with CPAM is closely monitored during pregnancy and the CPAM is removed via surgery after birth. Most babies with a CPAM are born without complication and are monitored during the first few months. Many patients have surgery, typically before their first birthday, because of the risk of recurrent lung infections associated with CPAMs. Some pediatric surgeons can safely remove these lesions using very tiny incisions using minimally invasive surgical techniques (thoracoscopy). However, some CPAM patients live a full life without any complication or incident. It is hypothesized that there are thousands of people living with an undetected CPAM. Through ultrasound testing employed in recent years, many more patients are aware that they live with this condition. Rarely, long standing CPAMs have been reported to become cancerous.

Very large cystic masses might pose a danger during birth because of the airway compression. In this situation, a special surgical type of delivery called the EXIT procedure may be used.

In rare extreme cases, where fetus's heart is in danger, fetal surgery can be performed to remove the CPAM. If non-immune hydrops fetalis develop, there is a near universal mortality of the fetus without intervention. Fetal surgery can improve the chances of survival to 50-60%. Recently, several studies found that a single course of prenatal steroids (betamethasone) may increase survival in hydropic fetuses with microcystic CPAMs to 75-100%. These studies indicate that large microcystic lesions may be treated prenatally without surgical intervention. Large macrocyst lesions may require in utero placement of a Harrison thoracoamniotic shunt.

Treatment ranges from simple enucleation of the cyst to curettage to resection. There are cysts—e.g., buccal bifurcation cyst—that resolve on their own, in which just close observation may be employed, unless it is infected and symptomatic.