Fetal and neonatal intestinal atresia are treated using laparotomy after birth. If the area affected is small, the surgeon may be able to remove the damaged portion and join the intestine back together. In instances where the narrowing is longer, or the area is damaged and cannot be used for period of time, a temporary stoma may be placed.

The differential diagnoses are extensive and include: Alagille syndrome, alpha-1-antitrypsin deficiency, Byler disease (progressive familial intrahepatic cholestasis), Caroli disease, choledochal cyst, cholestasis, congenital cytomegalovirus disease, congenital herpes simplex virus infection, congenital rubella, congenital syphilis, congenital toxoplasmosis, cystic fibrosis, galactosemia, idiopathic neonatal hepatitis, lipid storage disorders, neonatal hemochromatosis, and total parenteral nutrition-associated cholestasis.

Intestinal atresias are often discovered before birth: either during a routine sonogram which shows a dilated intestinal segment due to the blockage, or by the development of polyhydramnios (the buildup of too much amniotic fluid in the uterus). These abnormalities are indications that the fetus may have a bowel obstruction which a more detailed ultrasound study can confirm.

Some fetuses with bowel obstruction have abnormal chromosomes. An amniocentesis is recommended because it can determine not only the sex of the baby, but whether or not there is a problem with the chromosomes.

Diagnosis is made by an assessment of symptoms, physical exam, and medical history, in conjunction with blood tests, a liver biopsy, and imaging. Diagnosis is often made following investigation of prolonged jaundice that is resistant to phototherapy and/or exchange transfusions, with abnormalities in liver enzyme tests. Ultrasound or other forms of imaging can confirm the diagnosis. Further testing may include radioactive scans of the liver and a liver biopsy.

There is a risk of development of cancer with fundic gland polyposis, but it varies based on the underlying cause of the polyposis. The risk is highest with congenital polyposis syndromes, and is lowest in acquired causes. As a result, it is recommended that patients with multiple fundic polyps have a colonoscopy to evaluate the colon. If there are polyps seen on colonoscopy, genetic testing and testing of family members is recommended.

In the gastric adenocarcinoma associated with proximal polyposis of the stomach (GAPPS), there is a high risk of early development of proximal gastric adenocarcinoma.

It is still unclear which patients would benefit with surveillance gastroscopy, but most physicians recommend endoscopy every one to three years to survey polyps for dysplasia or cancer. In the event of high grade dysplasia, polypectomy, which is done through the endoscopy, or partial gastrectomy may be recommended. One study showed the benefit of NSAID therapy in regression of gastric polyps, but the efficacy of this strategy (given the side effects of NSAIDs) is still dubious.

The earliest point at which a CPAM can be detected is by prenatal ultrasound. The classic description is of an echogenic lung mass that gradually disappears over subsequent ultrasounds. The disappearance is due to the malformation becoming filled with fluid over the course of the gestation, allowing the ultrasound waves to penetrate it more easily and rendering it invisible on sonographic imaging. When a CPAM is rapidly growing, either solid or with a dominant cyst, they have a higher incidence of developing venous outflow obstruction, cardiac failure and ultimately "hydrops fetalis". If "hydrops" is not present, the fetus has a 95% chance of survival. When hydrops is present, risk of fetal demise is much greater without "in utero" surgery to correct the pathophysiology. The greatest period of growth is during the end of the second trimester, between 20–26 weeks.

A measure of mass volume divided by head circumference, termed cystic adenomatoid malformation volume ratio (CVR) has been developed to predict the risk of "hydrops". The lung mass volume is determined using the formula (length × width × anteroposterior diameter ÷ 2), divided by head circumference. With a CVR greater than 1.6 being considered high risk. Fetuses with a CVR less than 1.6 and without a dominant cyst have less than a 3% risk of hydrops. After delivery, if the patient is symptomatic, resection is mandated. If the infant is asymptomatic, the need for resection is a subject of debate, though it is usually recommended. Development of recurrent infections, rhabdomyosarcoma, adenocarcinomas "in situ" within the lung malformation have been reported.

Diagnosis is made through a combination of patient history, neurological examination, and medical imaging. Magnetic resonance imaging (MRI) is considered the best imaging modality for Chiari malformation since it visualizes neural tissue such as the cerebellar tonsils and spinal cord as well as bone and other soft tissues. CT and CT myelography are other options and were used prior to the advent of MRI, but they characterize syringomyelia and other neural abnormalities less well.

By convention the cerebellar tonsil position is measured relative to the basion-opisthion line, using sagittal T1 MRI images or sagittal CT images. The selected cutoff distance for abnormal tonsil position is somewhat arbitrary since not everyone will be symptomatic at a certain amount of tonsil displacement, and the probability of symptoms and syrinx increases with greater displacement, however greater than 5 mm is the most frequently cited cutoff number, though some consider 3–5 mm to be "borderline," and symptoms and syrinx may occur above that. One study showed little difference in cerebellar tonsil position between standard recumbent MRI and upright MRI for patients without a history of whiplash injury. Neuroradiological investigation is used to first rule out any intracranial condition that could be responsible for tonsillar herniation. Neuroradiological diagnostics evaluate the severity of crowding of the neural structures within the posterior cranial fossa and their impact on the foramen magnum. Chiari 1.5 is a term used when both brainstem and tonsillar herniation through the foramen magnum are present.

The diagnosis of a Chiari II malformation can be made prenatally through ultrasound.

In the late 19th century, Austrian pathologist Hans Chiari described seemingly related anomalies of the hindbrain, the so-called Chiari malformations I, II and III. Later, other investigators added a fourth (Chiari IV) malformation. The scale of severity is rated I – IV, with IV being the most severe. Types III and IV are very rare.

Other conditions sometimes associated with Chiari malformation include hydrocephalus, syringomyelia, spinal curvature, tethered spinal cord syndrome, and connective tissue disorders such as Ehlers-Danlos syndrome and Marfan syndrome.

Chiari malformation is the most frequently used term for this set of conditions. The use of the term Arnold–Chiari malformation has fallen somewhat out of favor over time, although it is used to refer to the type II malformation. Current sources use "Chiari malformation" to describe four specific types of the condition, reserving the term "Arnold-Chiari" for type II only. Some sources still use "Arnold-Chiari" for all four types.

Chiari malformation or Arnold–Chiari malformation should not be confused with Budd-Chiari syndrome, a hepatic condition also named for Hans Chiari.

In Pseudo-Chiari Malformation, Leaking of CSF may cause displacement of the cerebellar tonsils and similar symptoms sufficient to be mistaken for a Chiari I malformation.

Lymphatic malformations may be detected in the human fetus by ultrasound if they are of sufficient size. Detection of a cystic malformation may prompt further investigation, such as amniocentesis, in order to evaluate for genetic abnormalities in the fetus. Lymphatic malformations may be discovered postnatally or in older children/adults, and most commonly present as a mass or as an incidental finding during medical imaging.

Verification of the diagnosis may require more testing, as there are multiple cystic masses that arise in children. Imaging, such as ultrasound or MRI, may provide more information as to the size and extent of the lesion.

CPAMs are often identified during routine prenatal ultrasonography. Identifying characteristics on the sonogram include: an echogenic (bright) mass appearing in the chest of the fetus, displacement of the heart from its normal position, a flat or everted (pushed downward) diaphragm, or the absence of visible lung tissue.

CPAMs are classified into three different types based largely on their gross appearance. Type I has a large (>2 cm) multiloculated cysts. Type II has smaller uniform cysts. Type III is not grossly cystic, referred to as the "adenomatoid" type. Microscopically, the lesions are not true cysts, but communicate with the surrounding parenchyma. Some lesions have an abnormal connection to a blood vessel from an aorta and are referred to as "hybrid lesions."

A technetium-99m (99mTc) pertechnetate scan, also called Meckel scan, is the investigation of choice to diagnose Meckel's diverticula in children. This scan detects gastric mucosa; since approximately 50% of symptomatic Meckel's diverticula have ectopic gastric or pancreatic cells contained within them, this is displayed as a spot on the scan distant from the stomach itself. In children, this scan is highly accurate and noninvasive, with 95% specificity and 85% sensitivity; however, in adults the test is only 9% specific and 62% sensitive.

Patients with these misplaced gastric cells may experience peptic ulcers as a consequence. Therefore, other tests such as colonoscopy and screenings for bleeding disorders should be performed, and angiography can assist in determining the location and severity of bleeding. Colonoscopy might be helpful to rule out other sources of bleeding but it is not used as an identification tool. Angiography might identify brisk bleeding in patients with Meckel's diverticulum.

Ultrasonography could demonstrate omphaloenteric duct remnants or cysts. Computed tomography (CT scan) might be a useful tool to demonstrate a blind ended and inflamed structure in the mid-abdominal cavity, which is not an appendix.

In asymptomatic patients, Meckel's diverticulum is often diagnosed as an incidental finding during laparoscopy or laparotomy.

Treatment is surgical, potentially with a laparoscopic resection. In patients with bleeding, strangulation of bowel, bowel perforation or bowel obstruction, treatment involves surgical resection of both the Meckel's diverticulum itself along with the adjacent bowel segment, and this procedure is called a "small bowel resection". In patients without any of the aforementioned complications, treatment involves surgical resection of the Meckel's diverticulum only, and this procedure is called a simple diverticulectomy.

With regards to asymptomatic Meckel's diverticulum, some recommend that a search for Meckel's diverticulum should be conducted in every case of appendectomy/laparotomy done for acute abdomen, and if found, Meckel's diverticulectomy or resection should be performed to avoid secondary complications arising from it.

Assisted reproductive technology (ART) is a general term referring to methods used to achieve pregnancy by artificial or partially artificial means. According to the CDC, in general, ART procedures involve surgically removing eggs from a woman's ovaries, combining them with sperm in the laboratory, and returning them to the woman's body or donating them to another woman. ART has been associated with epigenetic syndromes, specifically BWS and Angelman syndrome. Three groups have shown an increased rate of ART conception in children with BWS. A retrospective case control study from Australia found a 1 in 4000 risk of BWS in their in-vitro population, several times higher than the general population. Another study found that children conceived by in vitro fertilisation (IVF) are three to four times more likely to develop the condition. No specific type of ART has been more closely associated with BWS. The mechanism by which ART produces this effect is still under investigation.

Treatment depends on the anatomy of the malformation as determined by angiography or Magnetic Resonance Imaging (MRI).

There is no cure for this condition. Treatment is supportive and varies depending on how symptoms present and their severity. Some degree of developmental delay is expected in almost all cases of M-CM, so evaluation for early intervention or special education programs is appropriate. Rare cases have been reported with no discernible delay in academic or school abilities.

Physical therapy and orthopedic bracing can help young children with gross motor development. Occupational therapy or speech therapy may also assist with developmental delays. Attention from an orthopedic surgeon may be required for leg length discrepancy due to hemihyperplasia.

Children with hemihyperplasia are thought to have an elevated risk for certain types of cancers. Recently published management guidelines recommend regular abdominal ultrasounds up to age eight to detect Wilms' tumor. AFP testing to detect liver cancer is not recommended as there have been no reported cases of hepatoblastoma in M-CM patients.

Congenital abnormalities in the brain and progressive brain overgrowth can result in a variety of neurological problems that may require intervention. These include hydrocephalus, cerebellar tonsillar herniation (Chiari I), seizures and syringomyelia. These complications are not usually congenital, they develop over time often presenting complications in late infancy or early childhood, though they can become problems even later. Baseline brain and spinal cord MRI imaging with repeat scans at regular intervals is often prescribed to monitor the changes that result from progressive brain overgrowth.

Assessment of cardiac health with echocardiogram and EKG may be prescribed and arrhythmias or abnormalities may require surgical treatment.

In general, the prognosis is very good. Children with BWS usually do very well and grow up to become the heights expected based on their parents' heights. While children with BWS are at increased risk of childhood cancer, most children with BWS do not develop cancer and the vast majority of children who do develop cancer can be treated successfully.

Children with BWS for the most part had no significant delays when compared to their siblings. However, some children with BWS do have speech problems that could be related to macroglossia or hearing loss.

Advances in treating neonatal complications and premature infants in the last twenty years have significantly improved the true infant mortality rate associated with BWS. In a review of pregnancies that resulted in 304 children with BWS, no neonatal deaths were reported. This is compared to a previously reported mortality rate of 20%. The data from the former study was derived from a BWS registry, a database that may be slightly biased towards involving living children; however, death was not an exclusion criterion to join the registry. This suggests that while infants with BWS are likely to have a higher than normal infant mortality risk, it may not be as high as 20%.

Gradient-Echo T2WI magnetic resonance imaging (MRI) is most sensitive method for diagnosing cavernous hemangiomas. MRI is such a powerful tool for diagnosis, it has led to an increase in diagnosis of cavernous hemangiomas since the technology's advent in the 1980s. The radiographic appearance is most commonly described as "popcorn" or "mulberry"-shaped. Computed tomography (CT) scanning is not a sensitive or specific method for diagnosing cavernous hemangiomas. Angiography is typically not necessary, unless it is required to rule out other diagnoses. Additionally, biopsies can be obtained from tumor tissue for examination under a microscope. It is essential to diagnose cavernous hemangioma because treatments for this benign tumor are less aggressive than that of cancerous tumors, such as angiosarcoma. However, since MRI appearance is practically pathognomonic, biopsy is rarely needed for verification.

Recent research has found that Dandy–Walker syndrome often occurs in patients with PHACES syndrome.

Treatment for individuals with Dandy–Walker Syndrome generally consists of treating the associated problems, if needed.

A special tube (shunt) to reduce intracranial pressure may be placed inside the skull to control swelling. Endoscopic third ventriculostomy is also an option.

Treatment may also consist of various therapies such as occupational therapy, physiotherapy, speech therapy or specialized education. Services of a teacher of students with blindness/visual impairment may be helpful if the eyes are affected.

Genetic counseling for VWS involves discussion of disease transmission in the autosomal dominant manner and possibilities for penetrance and expression in offspring. Autosomal dominance means affected parents have a 50% chance of passing on their mutated "IRF6" allele to a their child. Furthermore, if a cleft patient has lip pits, he or she has a ten times greater risk of having a child with cleft lip with or without cleft palate than a cleft patient who does not have lip pits. Types of clefting between parents and affected children are significantly associated; however, different types of clefts may occur horizontally and vertically within the same pedigree. In cases where clefting is the only symptom, a complete family history must be taken to ensure the patient does not have non-syndromic clefting.

Atresia is a condition in which an orifice or passage in the body is (usually abnormally) closed or absent.

Examples of atresia include:

- Biliary atresia, a condition in newborns in which the common bile duct between the liver and the small intestine is blocked or absent.

- Choanal atresia, blockage of the back of the nasal passage, usually by abnormal bony or soft tissue.

- Esophageal atresia, which affects the alimentary tract and causes the esophagus to end before connecting normally to the stomach.

- Imperforate anus, malformation of the opening between the rectum and anus.

- Intestinal atresia, malformation of the intestine, usually resulting from a vascular accident in utero.

- Microtia, absence of the ear canal or failure of the canal to be tubular or fully formed (can be related to Microtia, a congenital deformity of the pinna, or outer ear).

- Ovarian follicle atresia, the degeneration and subsequent resorption of one or more immature ovarian follicles.

- Potter sequence, congenital decreased size of the kidney leading to absolutely no functionality of the kidney, usually related to a single kidney.

- Pulmonary atresia, malformation of the pulmonary valve in which the valve orifice fails to develop.

- Renal agenesis, only having one kidney.

- Tricuspid atresia, a form of congenital heart disease whereby there is a complete absence of the tricuspid valve, and consequently an absence of the right atrioventricular connection.

- Vaginal atresia, a congenital occlusion of the vagina or subsequent adhesion of the walls of the vagina, resulting in its occlusion.

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

Prognosis varies widely depending on severity of symptoms, degree of intellectual impairment, and associated complications. Because the syndrome is rare and so newly identified, there are no long term studies.

Fundic gland polyposis is a medical syndrome where the fundus and the body of the stomach develop many polyps. The condition has been described both in patients with familial adenomatous polyposis (FAP) and attenuated variants (AFAP), and in patients in whom it occurs sporadically.

Attempts must be made to determine whether there is a secondary cause amenable to treatment.

Primary (idiopathic) intestinal pseudo-obstruction is diagnosed based on motility studies, x-rays and gastric emptying studies.