Very few risk factors for choanal atresia have been identified. While causes are unknown, both genetic and environmental triggers are suspected. One study suggests that chemicals that act as endocrine disrupters may put an unborn infant at risk. A 2012 epidemiological study looked at atrazine, a commonly used herbicide in the U.S., and found that women who lived in counties in Texas with the highest levels of this chemical being used to treat agricultural crops were 80 times more likely to give birth to infants with choanal atresia or stenosis compared to women who lived in the counties with the lowest levels. Another epidemiological report in 2010 found even higher associations between increased incidents of choanal atresia and exposure to second-hand-smoke, coffee consumption, high maternal zinc and B-12 intake and exposure to anti-infective urinary tract medications.

Choanal atresia can be suspected if it is impossible to insert a nasal catheter.

Also, if one notices a continuous stream of mucus draining from one or both nostrils, it could be a sign of an atresia. Another common sign is cyanosis in an infant while breast feeding, as breathing is dependent on nasal patency in this situation.

Diagnosis is confirmed by radiological imaging, usually CT scan.

This condition may be visible, after about 26 weeks, on an ultrasound. On antenatal USG, the finding of an absent or small stomach in the setting of polyhydramnios was considered a potential symptom of esophageal atresia. However, these findings have a low positive predictive value. The upper neck pouch sign is another sign that helps in the antenatal diagnosis of esophageal atresia and it may be detected soon after birth as the affected infant will be unable to swallow its own saliva. Also, the newborn can present with gastric distention, cough, apnea, tachypnea, and cyanosis. In many types of esophageal atresia, a feeding tube will not pass through the esophagus.

This condition takes several different forms, often involving one or more fistulas connecting the trachea to the esophagus (tracheoesophageal fistula).

It is surgically corrected, with resection of any fistula and anastomosis of any discontinuous segments.

Fistulae between the trachea and esophagus in the newborn can be of diverse morphology and anatomical location; however, various pediatric surgical publications have attempted a classification system based on the below specified types.

Not all types include both esophageal agenesis and tracheoesophageal fistula, but the most common types do.

The letter codes are usually associated with the system used by Gross, while number codes are usually associated with Vogt.

An additional type, "blind upper segment only" has been described, but this type is not usually included in most classifications.

Patients with abnormal cardiac and kidney function may be more at risk for hemolytic uremic syndrome

When an infant is born with an anorectal malformation, it is usually detected quickly as it is a very obvious defect. Doctors will then determine the type of birth defect the child was born with and whether or not there are any associated malformations. It is important to determine the presence of any associated defects during the newborn period in order to treat them early and avoid further sequelae. There are two main categories of anorectal malformations: those that require a protective colostomy and those that do not. The decision to open a colostomy is usually taken within the first 24 hours of birth.

Sonography can be used to determine the type of imperforate anus.

Suspicion of a chromosome abnormality is typically raised due to the presence of developmental delays or birth defects. Diagnosis of distal 18q- is usually made from a blood sample. A routine chromosome analysis, or karyotype, is usually used to make the initial diagnosis, although it may also be made by microarray analysis. Increasingly, microarray analysis is also being used to clarify breakpoints. Prenatal diagnosis is possible using amniocentesis or chorionic villus sampling.

Imperforate anus usually requires immediate surgery to open a passage for feces unless a fistula can be relied on until corrective surgery takes place. Depending on the severity of the imperforate, it is treated either with a perineal anoplasty or with a colostomy.

While many surgical techniques to definitively repair anorectal malformations have been described. The posterior sagittal approach (PSARP) has become the most popular. It involves dissection of the perineum without entry into the abdomen and 90% of defects in boys can be repaired this way.

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.

At present, treatment for distal 18q- is symptomatic, meaning the focus is on treating the signs and symptoms of the conditions as they arise. To ensure early diagnosis and treatment, people with distal 18q- are suggested to undergo routine screenings for thyroid, hearing, and vision problems.

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.

Alagille syndrome can be determined by a special kind of newborn screening wherein DNA samples are analyzed for markers in the JAG1 section. The DNA sequence patterns of a child will be analyzed for probabilistic deletions and therefore takes weeks to complete. After detection, the child should be treated with vitamins and necessary diet to develop the liver function postnatally.

Early treatment includes removing fluids from the stomach via a nasogastric tube, and providing fluids intravenously. The definitive treatment for duodenal atresia is surgery (duodenoduodenostomy), which may be performed openly or laparoscopically. The surgery is not urgent. The initial repair has a 5 percent morbidity and mortality rate.

The incidence of VACTERL association is estimated to be approximately 1 in 10,000 to 1 in 40,000 live-born infants. It is seen more frequently in infants born to diabetic mothers. While most cases are sporadic, there are clearly families who present with multiple involved members.

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.

Typically, testing is first done to determine the quality of hearing. This can be done as early as in the first two weeks with a BAER test (Brain Stem Auditory Response Test). At age 5–6, CT or CAT scans of the middle ear can be done to elucidate its development and clarify which patients are appropriate candidates for surgery to improve hearing. For younger individuals, this is done under sedation.

The hearing loss associated with congenital aural atresia is a conductive hearing loss—hearing loss caused by inefficient conduction of sound to the inner ear. Essentially, children with aural atresia have hearing loss because the sound cannot travel into the (usually) healthy inner ear—there is no ear canal, no eardrum, and the small ear bones (malleus/hammer, incus/anvil, and stapes/stirrup) are underdeveloped. "Usually" is in parentheses because rarely, a child with atresia also has a malformation of the inner ear leading to a sensorineural hearing loss (as many as 19% in one study). Sensorineural hearing loss is caused by a problem in the inner ear, the cochlea. Sensorineural hearing loss is not correctable by surgery, but properly fitted and adjusted hearing amplification (hearing aids) generally provide excellent rehabilitation for this hearing loss. If the hearing loss is severe to profound in both ears, the child may be a candidate for a cochlear implant (beyond the scope of this discussion).

Unilateral sensorineural hearing loss was not generally considered a serious disability by the medical establishment before the nineties; it was thought that the afflicted person was able to adjust to it from birth. In general, there are exceptional advantages to gain from an intervention to enable hearing in the microtic ear, especially in bilateral microtia. Children with untreated unilateral sensorineural hearing loss are more likely to have to repeat a grade in school and/or need supplemental services (e.g., FM system – see below) than their peers.

Children with unilateral sensorineural hearing loss often require years of speech therapy in order to learn how to enunciate and understand spoken language. What is truly unclear, and the subject of an ongoing research study, is the effect of unilateral conductive hearing loss (in children with unilateral aural atresia) on scholastic performance. If atresia surgery or some form of amplification is not used, special steps should be taken to ensure that the child is accessing and understanding all of the verbal information presented in school settings. Recommendations for improving a child's hearing in the academic setting include preferential seating in class, an FM system (the teacher wears a microphone, and the sound is transmitted to a speaker at the child's desk or to an ear bud or hearing aid the child wears), a bone-anchored hearing aid (BAHA), or conventional hearing aids. Age for BAHA implantation depends on whether the child is in Europe (18 months) or the US (age 5). Until then it is possible to fit a BAHA on a softband

It is important to note that not all children with aural atresia are candidates for atresia repair. Candidacy for atresia surgery is based on the hearing test (audiogram) and CT scan imaging. If a canal is built where one does not exist, minor complications can arise from the body's natural tendency to heal an open wound closed. Repairing aural atresia is a very detailed and complicated surgical procedure which requires an expert in atresia repair. While complications from this surgery can arise, the risk of complications is greatly reduced when using a highly experienced otologist. Atresia patients who opt for surgery will temporarily have the canal packed with gelatin sponge and silicone sheeting to prevent closure. The timing of ear canal reconstruction (canalplasty) depends on the type of external ear (Microtia) repair desired by the patient and family. Two surgical teams in the USA are currently able to reconstruct the canal at the same time as the external ear in a single surgical stage (one stage ear reconstruction).

In cases where a later surgical reconstruction of the external ear of the child might be possible, positioning of the BAHA implant is critical. It may be necessary to position the implant further back than usual to enable successful reconstructive surgery – but not so far as to compromise hearing performance. If the reconstruction is ultimately successful, it is easy to remove the percutaneous BAHA abutment. If the surgery is unsuccessful, the abutment can be replaced and the implant re-activated to restore hearing.

Aural atresia is the underdevelopment of the middle ear and canal and usually occurs in conjunction with microtia. Atresia occurs because patients with microtia may not have an external opening to the ear canal, though. However, the cochlea and other inner ear structures are usually present. The grade of microtia usually correlates to the degree of development of the middle ear.

Microtia is usually isolated, but may occur in conjunction with hemifacial microsomia, Goldenhar Syndrome or Treacher-Collins Syndrome. It is also occasionally associated with kidney abnormalities (rarely life-threatening), and jaw problems, and more rarely, heart defects and vertebral deformities.

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.

Suspicion of a chromosome abnormality is typically raised due to the presence of developmental delays or birth defects. Diagnosis of ring 18 is usually made via a blood sample. A routine chromosome analysis, or karyotype, is usually used to make the initial diagnosis, although it may also be made by microarray analysis. Increasingly, microarray analysis is also being used to clarify breakpoints. Prenatal diagnosis is possible via amniocentesis or chorionic villus sampling.

The outcome of Potter's Sequence is poor. A series of 23 patients in 2007 recorded 7 deaths, 4 in the neonatal period. All 16 survivors have chronic kidney disease, with half developing end stage renal failure (median age 0.3 years, range 2 days to 8.3 years). Survivors had growth impairment (44%) and cognitive and motor development delay (25%)

The first child to survive Bilateral Renal Agenesis (BRA), Abigail Rose Herrera Beutler, was born on July 2013 to US Congresswoman Jaime Herrera Beutler.

A few weeks before she was born, Dr. Jessica Bienstock, a professor of maternal-fetal medicine at Johns Hopkins Hospital, administered a series of saline solution injections into the mother's womb to help the baby's lungs to develop. After Abigail was born, the procedure was considered a success. The infant did not need artificial respiration and could breathe on her own. Her parents kept her on kidney dialysis at home until old enough for a kidney transplant. On February 8, 2016, at the age of two, Abigail received a kidney from her father at the Lucile Packard Children's Hospital Stanford in California.

The prognosis for vaginal atresia is one that is complicated. There are variations in patients' anatomic findings as well as an absence in consistent surgical techniques which makes it difficult to give a prognosis for this condition. Along with other conditions that give rise to an abnormal perineum (i.e. ambiguous genitalia and other various abnormalities that range from cloaca to urogenital sinus), individuals with vaginal atresia often report reconstruction as an outcome of treatment. Due to this, it is difficult to compare outcomes between individuals with vaginal atresia.

In regards to the diagnosis of pulmonary atresia the body requires oxygenated blood for survival. pulmonary atresia is not threatening to a developing fetus however, because the mother's placenta provides the needed oxygen since the baby's lungs are not yet functional. Once the baby is born its lungs must now provide the oxygen needed for survival, but with pulmonary atresia there is no opening on the pulmonary valve for blood to get to the lungs and become oxygenated. Due to this, the newborn baby is blue in color and pulmonary atresia can usually be diagnosed within hours or minutes after birth.

The diagnosis of pulmonary atresia can be done via the following exams/methods: an echocardiogram, chest x-ray, EKG and an exam to measure the amount of in the body.

During pregnancy, duodenal atresia is associated with increased amniotic fluid in the uterus, which is called polyhydramnios. This increase in amniotic fluid is caused by the inability of the fetus to swallow the amniotic fluid and absorb it in their digestive tract.

After birth, duodenal atresia may cause abdominal distension, especially of the upper abdomen. Bilious vomiting commonly occurs within the first day of life. The vomiting is described as "bilious", because it contains bile acid.