The goal of newborn screening programs is to detect and start treatment within the first 1–2 weeks of life. Treatment consists of a daily dose of thyroxine, available as a small tablet. The generic name is levothyroxine, and several brands are available. The tablet is crushed and given to the baby with a small amount of water or milk. The most commonly recommended dose range is 10-15 μg/kg daily, typically 12.5 to 37.5 or 44 μg.

Within a few weeks, the T and TSH levels are rechecked to confirm that they are being normalized by treatment. As the child grows up, these levels are checked regularly to maintain the right dose. The dose increases as the child grows.

Most children born with congenital hypothyroidism and correctly treated with thyroxine grow and develop normally in all respects. Even most of those with athyreosis and undetectable T levels at birth develop with normal intelligence, although as a population academic performance tends to be below that of siblings and mild learning problems occur in some.

Congenital hypothyroidism is the most common preventable cause of intellectual disability. Few treatments in the practice of medicine provide as large a benefit for as small an effort.

The developmental quotient (DQ, as per Gesell Developmental Schedules) of children with hypothyroidism at age 24 months that have received treatment within the first 3 weeks of birth is summarised below:

Around 5 years of age, surgical correction may be necessary to prevent any worsening of the deformity. If the mother has dysplasia, caesarian delivery may be necessary. Craniofacial surgery may be necessary to correct skull defects. Coxa vara is treated by corrective femoral osteotomies. If there is brachial plexus irritation with pain and numbness, excision of the clavicular fragments can be performed to decompress it. In case of open fontanelle, appropriate headgear may be advised by the orthopedist for protection from injury.

Several studies have reported that life expectancy appears to be normal for people with CCD.

No treatment is required, but neoplastic processes (metastatic maliganancy to the submandibular lymph nodes and/or salivary gland tumours) should be ruled out. This is usually done with clinical exam and imaging. Very rarely, since the defect contains salivary gland tissue, salivary gland tumors can occur within an established defect but there is likely no difference in the risk of neoplasia in salivary gland tissue at other sites.

Osteofibrous dysplasia is treated with marginal resection with or without bone grafting, depending on the size of the lesion and the extent of bony involvement. However, due to the high rate of recurrence in skeletally immature individuals, this procedure is usually postponed until skeletal maturity.

Simple cholecystectomy is suitable for type I patients. For types II–IV, subtotal cholecystectomy can be performed to avoid damage to the main bile ducts. Cholecystectomy and bilioenteric anastomosis may be required. Roux-en-Y hepaticojejunostomy has shown good outcome in some studies.

The primary aim of treatment of a newly formed oroantral communication is to prevent the development of an oroantral fistula as well as chronic sinusitis. The decision on how to treat OAC/OAF depends on various factors. Small size communications between 1 and 2 mm in diameter, if uninfected, are likely to form a clot and heal by itself later. Communications larger than this require treatments to close the defect and these interventions can be categorised into 3 types: surgical, non-surgical and pharmacological.

Congenital disorder of glycosylation type IIc or Leukocyte adhesion deficiency-2 (LAD2) is a type of leukocyte adhesion deficiency attributable to the absence of neutrophil sialyl-LewisX, a ligand of P- and E-selectin on vascular endothelium. It is associated with "SLC35C1".

This disorder was discovered in two unrelated Israeli boys 3 and 5 years of age, each the offspring of consanguineous parents. Both had severe mental retardation, short stature, a distinctive facial appearance, and the Bombay (hh) blood phenotype, and both were secretor- and Lewis-negative. They both had had recurrent severe bacterial infections similar to those seen in patients with LAD1, including pneumonia, peridontitis, otitis media, and localized cellulitis. Similar to that in patients with LAD1, their infections were accompanied by pronounced leukocytosis (30,000 to 150,000/mm) but an absence of pus formation at sites of recurrent cellulitis. In vitro studies revealed a pronounced defect in neutrophil motility. Because the genes for the red blood cell H antigen and for the secretor status encode for distinct α1,2-fucosyltransferases and the synthesis of Sialyl-LewisX requires an α1,3-fucosyltransferase, it was postulated that a general defect in fucose metabolism is the basis for this disorder. It was subsequently found that GDP-L-fucose transport into Golgi vesicles was specifically impaired, and then missense mutations in the GDP-fucose transporter cDNA of three patients with LAD2 were discovered. Thus, GDP-fucose transporter deficiency is a cause of LAD2.

Osteoporosis is due to causal factors like atrophy of disuse and gonadal deficiency. Hence osteoporosis is common in post menopausal women and in men above 50 yrs. Hypercorticism may also be causal factor, as osteoporosis may be seen as a feature of Cushing's syndrome.

The treatment aims are to eliminate the bacteria from the exposed surface of the root(s) and to establish the anatomy of the tooth, so that better plaque control can be achieved. Treatment plans for patients differ depending on the local and anatomical factors.

For Grade I furcation, scaling and polishing, root surface debridement or furcationplasty could be done if suitable.

For Grade II furcation, furcationplasty, open debridement, tunnel preparation, root resection, extraction, guided tissue regeneration (GTR) or enamel matrix derivative could be considered.

As for Grade III furcation, open debridement, tunnel preparation, root resection, GTR or tooth extraction could be performed if appropriate.

Tooth extraction is usually considered if there is extensive loss of attachment or if other treatments will not obtain good result (i.e. achieving a nice gingival contour to allow good plaque control).

The treatment of pentalogy of Cantrell is directed toward the specific symptoms that are apparent in each individual. Surgical intervention for cardiac, diaphragmatic and other associated defects is necessary. Affected infants will require complex medical care and may require surgical intervention. In most cases, pentalogy of Cantrell is fatal without surgical intervention. However, in some cases, the defects are so severe that the individual dies regardless of the medical or surgical interventions received.

The specific treatment strategy will vary from one infant to another based upon various factors, including the size and type of abdominal wall defect, the specific cardiac anomalies that are present, and the particular type of ectopia cordis. Surgical procedures that may be required shortly after birth include repair of an omphalocele. At this time, physicians may also attempt to repair certain other defects including defects of the sternum, diaphragm and the pericardium.

In severe cases, some physicians advocate for a staged repair of the defects associated with pentalogy of Cantrell. The initial operation immediately after birth provides separation of the peritoneal and pericardial cavities, coverage of the midline defect and repair of the omphalocele. After appropriate growth of the thoracic cavity and lungs, the second stage consists of the repair of cardiac defects and return of the heart to the chest. Eventually, usually by age 2 or 3, reconstruction of the lower sternum or epigastrium may be necessary.

Other treatment of pentalogy of Cantrell is symptomatic and supportive.

Metabolic bone disease is an umbrella term referring to abnormalities of bones caused by a broad spectrum of disorders.

Most commonly these disorders are caused by abnormalities of minerals such as calcium, phosphorus, magnesium or vitamin D leading to dramatic clinical disorders that are commonly reversible once the underlying defect has been treated. These disorders are to be differentiated from a larger group of genetic bone disorders where there is a defect in a specific signaling system or cell type that causes the bone disorder. There may be overlap. For example, genetic or hereditary hypophosphatemia may cause the metabolic bone disorder osteomalacia. Although there is currently no treatment for the genetic condition, replacement of phosphate often corrects or improves the metabolic bone disorder.

Microcoria is a congenital disease in which the pupils of the subject are narrower than 2 mm in diameter. Microcoria is associated with juvenile-onset glaucoma. It is also associated with Pierson syndrome chararacterized by microcoria and congenital nephrotic syndrome. The defect is in the Laminin beta 2 gene on chromosome 3p21 which encodes a protein essential to the glomerular basement membrane.

It is also part of the known manifestations of a born infant to a mother suffering from uncontrolled hyperglycemia. Other symptoms include transposition of great vessels, respiratory distress secondary to surfactant defect, sacral agensis, jitteriness, irritability, and lethargy due to rebound fetal hypoglycemia. Congenital microcoria is an autosomal dominant trait. However, it can also occur sporadically.

If the inciting defect in the heart is identified "before" it causes significant pulmonary hypertension, it can normally be repaired through surgery, preventing the disease. After pulmonary hypertension is sufficient to reverse the blood flow through the defect, however, the maladaptation is considered irreversible, and a heart–lung transplant or a lung transplant with repair of the heart is the only curative option.

Transplantation is the final therapeutic option and only for patients with poor prognosis and quality of life. Timing and appropriateness of transplantation remain difficult decisions. 5-year and 10-year survival ranges between 70% and 80%, 50% and 70%, 30% and 50%, respectively. Since the average life expectancy of patients after lung transplantation is as low as 30% at 5 years, patients with "reasonable functional status" related to Eisenmenger syndrome have "improved survival with conservative medical care" compared with transplantation.

Various medicines and therapies for pulmonary hypertension are under investigation for treatment of the symptoms.

The Stafne defect (also termed Stafne's idiopathic bone cavity, Stafne bone cavity, Stafne bone cyst (misnomer), lingual mandibular salivary gland depression, lingual mandibular cortical defect, latent bone cyst, or static bone cyst) is a depression of the mandible on the lingual surface (the side nearest the tongue). The Stafne defect is thought to be a normal anatomical variant, as the depression is created by ectopic salivary gland tissue associated with the submandibular gland and does not represent a pathologic lesion as such.

Medications may be needed as an adjunct to assist the closure of the defect. Antibiotics can help control or prevent any sinus infections. Preoperative nasal decongestants usage can reduce any existing sinus inflammation which will aid surgical manipulation of the mucosa over the bone.

Management of sickle nephropathy is not separate from that of overall patient management. In addition, however, the use of ACE inhibitors has been associated with improvement of the hyperfiltration glomerulopathy. Three-year graft and patient survival in kidney transplant recipients with sickle nephropathy is lower when compared to those with other causes of end-stage kidney disease.

Colobomas of the iris may be treated in a number of ways. A simple cosmetic solution is a specialized cosmetic contact lens with an artificial pupil aperture. Surgical repair of the iris defect is also possible. Surgeons can close the defect by stitching in some cases. More recently artificial iris prosthetic devices such as the Human Optics artificial iris have been used successfully by specialist surgeons. This device cannot be used if the natural lens is in place and is not suitable for children. Suture repair is a better option where the lens is still present.

Vision can be improved with glasses, contact lenses or even laser eye surgery but may be limited if the retina is affected or there is amblyopia.

Treatment is surgical and involves closure of the atrial and ventricular septal defects and restoration of a competent left AV valve as far as is possible. Open surgical procedures require a heart-lung machine and are done with a median sternotomy. Surgical mortality for uncomplicated ostium primum defects in experienced centers is 2%; for uncomplicated cases of complete atrioventricular canal, 4% or less. Certain complications such as tetralogy of Fallot or highly unbalanced flow across the common AV valve can increase risk significantly.

Infants born with AVSD are generally in sufficient health to not require immediate corrective surgery. If surgery is not required immediately after birth, the newborn will be closely monitored for the next several months, and the operation held-off until the first signs of lung distress or heart failure. This gives the infant time to grow, increasing the size of, and thereby the ease of operation on, the heart, as well as the ease of recovery. Infants will generally require surgery within three to six months, however, they may be able to go up to two years before the operation becomes necessary, depending on the severity of the defect.

Sometimes CHD improves without treatment. Other defects are so small that they do not require any treatment. Most of the time CHD is serious and requires surgery and/or medications. Medications include diuretics, which aid the body in eliminating water, salts, and digoxin for strengthening the contraction of the heart. This slows the heartbeat and removes some fluid from tissues. Some defects require surgical procedures to restore circulation back to normal and in some cases, multiple surgeries are needed.

Interventional cardiology now offers patients minimally invasive alternatives to surgery for some patients. The Melody Transcatheter Pulmonary Valve (TPV), approved in Europe in 2006 and in the U.S. in 2010 under a Humanitarian Device Exemption (HDE), is designed to treat congenital heart disease patients with a dysfunctional conduit in their right ventricular outflow tract (RVOT). The RVOT is the connection between the heart and lungs; once blood reaches the lungs, it is enriched with oxygen before being pumped to the rest of the body. Transcatheter pulmonary valve technology provides a less-invasive means to extend the life of a failed RVOT conduit and is designed to allow physicians to deliver a replacement pulmonary valve via a catheter through the patient’s blood vessels.

Most patients require lifelong specialized cardiac care, first with a pediatric cardiologist and later with an adult congenital cardiologist. There are more than 1.8 million adults living with congenital heart defects.

Tracheal agenesis is a rare birth defect with a prevalence of less than 1 in 50,000, in which the trachea fails to develop. The defect is normally fatal, although occasional cases have been reported of long-term survival following surgical intervention.

There are three main types of tracheal agenesis, designated Types I, II and III.

In 2013, a case was reported of a South Korean child with tracheal agenesis who had been successfully treated after having been kept alive in an intensive care unit for the first two and a half years of her life. She then had an artificially created trachea implanted that had been created by tissue engineering using her own stem cells. The patient however later died from complications.

Simple l-TGA has a very good prognosis, with many individuals being asymptomatic and not requiring surgical correction.

In a number of cases, the (technically challenging) "double switch operation" has been successfully performed to restore the normal blood flow through the ventricles.

The treatment of pulmonary atresia consists of: an IV medication called prostaglandin E1, which is used for treatment of pulmonary atresia, as it stops the ductus arteriosus from closing, allowing mixing of the pulmonary and systemic circulations, but prostaglandin E1 can be dangerous as it can cause apnea. Another example of preliminary treatment is heart catheterization to evaluate the defect or defects of the heart; this procedure is much more invasive. Ultimately, however, the individual will need to have a series of surgeries to improve the blood flow permanently. The first surgery will likely be performed shortly after birth. A shunt can be created between the aorta and the pulmonary artery to help increase blood flow to the lungs. As the child grows, so does the heart and the shunt may need to be revised in order to meet the body's requirements.

The type of surgery recommended depends on the size of the right ventricle and the pulmonary artery, if the right ventricle is small and unable to act as a pump, the surgery performed would be the Fontan procedure. In this three-stage procedure, the right atrium is disconnected from the pulmonary circulation. The systemic venous return goes directly to the lungs, by-passing the heart.Very young children with elevated pulmonary vascular resistance may not able to undergo the Fontan procedure. Cardiac catheterization may be done to determine the resistance before going ahead with the surgery.

Treatment options range from no treatment for a mild cystocele to surgery for a more extensive cystocele. If a cystocele is not bothersome, the clinician may only recommend avoiding heavy lifting or straining that could cause the cystocele to worsen. If symptoms are moderately bothersome, the doctor may recommend a pessary, a device placed in the vagina to hold the bladder in place. Treatment can consist of a combination of non-surgical and surgical management. Treatment choice is also related to age, desire to have children, severity of impairment, desire to continue sexual intercourse and other diseases that a woman may have.