A low socioeconomic status in a deprived neighborhood may include exposure to “environmental stressors and risk factors.” Socioeconomic inequalities are commonly measured by the Cartairs-Morris score, Index of Multiple Deprivation, Townsend deprivation index, and the Jarman score. The Jarman score, for example, considers “unemployment, overcrowding, single parents, under-fives, elderly living alone, ethnicity, low social class and residential mobility.” In Vos’ meta-analysis these indices are used to view the effect of low SES neighborhoods on maternal health. In the meta-analysis, data from individual studies were collected from 1985 up until 2008. Vos concludes that a correlation exists between prenatal adversities and deprived neighborhoods. Other studies have shown that low SES is closely associated with the development of the fetus in utero and growth retardation. Studies also suggest that children born in low SES families are “likely to be born prematurely, at low birth weight, or with asphyxia, a birth defect, a disability, fetal alcohol syndrome, or AIDS.” Bradley and Corwyn also suggest that congenital disorders arise from the mother’s lack of nutrition, a poor lifestyle, maternal substance abuse and “living in a neighborhood that contains hazards affecting fetal development (toxic waste dumps).” In a meta-analysis that viewed how inequalities influenced maternal health, it was suggested that deprived neighborhoods often promoted behaviors such as smoking, drug and alcohol use. After controlling for socioeconomic factors and ethnicity, several individual studies demonstrated an association with outcomes such as perinatal mortality and preterm birth.

Substances whose toxicity can cause congenital disorders are called "teratogens", and include certain pharmaceutical and recreational drugs in pregnancy as well as many environmental toxins in pregnancy.

A review published in 2010 identified 6 main teratogenic mechanisms associated with medication use: folate antagonism, neural crest cell disruption, endocrine disruption, oxidative stress, vascular disruption and specific receptor- or enzyme-mediated teratogenesis.

It is estimated that 10% of all birth defects are caused by prenatal exposure to a teratogenic agent. These exposures include, but are not limited to, medication or drug exposures, maternal infections and diseases, and environmental and occupational exposures. Paternal smoking use has also been linked to an increased risk of birth defects and childhood cancer for the offspring, where the paternal germline undergoes oxidative damage due to cigarette use. Teratogen-caused birth defects are potentially preventable. Studies have shown that nearly 50% of pregnant women have been exposed to at least one medication during gestation. During pregnancy, a female can also be exposed to teratogens from the contaminated clothing or toxins within the seminal fluid of a partner. An additional study found that of 200 individuals referred for genetic counseling for a teratogenic exposure, 52% were exposed to more than one potential teratogen.

In a newborn boy thought to have Fryns syndrome, Clark and Fenner-Gonzales (1989) found mosaicism for a tandem duplication of 1q24-q31.2. They suggested that the gene for this disorder is located in that region. However, de Jong et al. (1989), Krassikoff and Sekhon (1990), and Dean et al. (1991) found possible Fryns syndrome associated with anomalies of chromosome 15, chromosome 6, chromosome 8(human)and chromosome 22, respectively. Thus, these cases may all represent mimics of the mendelian syndrome and have no significance as to the location of the gene for the recessive disorder.

By array CGH, Slavotinek et al. (2005) screened patients with DIH and additional phenotypic anomalies consistent with Fryns syndrome for cryptic chromosomal aberrations. They identified submicroscopic chromosome deletions in 3 probands who had previously been diagnosed with Fryns syndrome and had normal karyotyping with G-banded chromosome analysis. Two female infants were found to have microdeletions involving 15q26.2 (see 142340), and 1 male infant had a deletion in band 8p23.1 (see 222400).

In France, Aymé, "et al." (1989) estimated the prevalence of Fryns syndrome to be 0.7 per 10,000 births based on the diagnosis of 6 cases in a series of 112,276 consecutive births (live births and perinatal deaths).

Studies have shown that obesity of the mother increases the risk of neural tube disorders such as iniencephaly by 1.7 fold while severe obesity increases the risk by over 3 fold.

Once a mother has given birth to a child with iniencephaly, risk of reoccurrence increases to 1-5%.

Pancreas divisum in individuals with no symptoms does not require treatment. Treatment of those with symptoms varies and has not been well established. A surgeon may attempt a sphincterotomy by cutting the minor papilla to enlarge the opening and allow pancreatic enzymes to flow normally. During surgery, a stent may be inserted into the duct to ensure that the duct will not close causing a blockage. This surgery can cause pancreatitis in patients, or in rare cases, kidney failure and death.

An association with adenoma of the minor papilla has been reported.

These lesions usually present in neonates, although they may not come to clinical attention until adulthood (for cosmetic reasons). There is no gender predilection. They are present in approximately 3-6 per 1000 live births.

The female homolog to the male verumontanum from which the valves originate is the hymen.

Pancreaticobiliary maljunction is a congenital malformation, in which the pancreatic and bile ducts join anatomically outside the duodenal wall, forming a markedly long common channel. This anomaly prevents normal control by the sphincter of Oddi located in the duodenal wall, allowing regurgitation of pancreatic juices into the biliary tract and possibly leading to a higher probability of pancreaticobiliary cancers.

Known environmental factors include certain infections during pregnancy such as Rubella, drugs (alcohol, hydantoin, lithium and thalidomide) and maternal illness (diabetes mellitus, phenylketonuria, and systemic lupus erythematosus).

Being overweight or obese increases the risk of congenital heart disease. Additionally, as maternal obesity increases, the risk of heart defects also increases. A distinct physiological mechanism has not been identified to explain the link between maternal obesity and CHD, but both prepregnancy folate deficiency and diabetes have been implicated in some studies.

Toxic megacolon is mainly seen in ulcerative colitis and pseudomembranous colitis, two chronic inflammations of the colon (and occasionally, in the other type of inflammatory bowel disease, Crohn's disease). Its mechanism is incompletely understood. It is probably due to an excessive production of nitric oxide, at least in ulcerative colitis. The prevalence is about the same for both sexes.

In patients with HIV/AIDS, cytomegalovirus (CMV) colitis is the leading cause of toxic megacolon and emergency laparotomy. CMV may also increase the risk of toxic megacolon in non-HIV/AIDS patients with IBD.

A majority of individuals born with pancreas divisum will not have symptoms. In some cases, pancreas divisum is only detected during autopsy. A small group of individuals will develop symptoms which commonly include abdominal pain, nausea, vomiting, and acute and chronic pancreatitis.

The cause of congenital heart disease may be genetic, environmental, or a combination of both.

Risperidone, an anti-psychotic medication, can result in megacolon.

The condition arises from some factor or set of factors present during approximately the 3rd week to 7th week of fetal development. Formation of the sacrum/lower back and corresponding nervous system is usually nearing completion by the 4th week of development. Due to abnormal gastrulation, the mesoderm migration is disturbed. This disturbance results in symptoms varying from minor lesions of the lower vertebrae to more severe symptoms such as complete fusion of the lower limbs. While the exact cause is unknown, it has been speculated that the condition may be associated with certain dietary deficiencies including a lack or insufficient amounts of folic acid.

Sacral agenesis syndrome (agenesis of the lumbar spine, sacrum, and coccyx, and hypoplasia of the lower extremities) is a well-established congenital anomaly associated with maternal diabetes mellitus (not gestational diabetes). However, other causes are presumably involved, as demonstrated by the rare incidence of caudal regression syndrome (1:60,000) compared to diabetes.

The dominant inherited sacral agenesis (also referred to as Currarino syndrome) is very often correlated with a mutation in the Hb9 (also called HlxB9) gene (shown by Sally Ann Lynch, 1995, Nature Genetics).

It may be the cause of sirenomelia ("Mermaid syndrome").

Posterior urethral valve (PUV) disorder is an obstructive developmental anomaly in the urethra and genitourinary system of male newborns. A posterior urethral valve is an obstructing membrane in the posterior male urethra as a result of abnormal "in utero" development. It is the most common cause of bladder outlet obstruction in male newborns. The disorder varies in degree, with mild cases presenting late due to milder symptoms. More severe cases can have renal and respiratory failure from lung underdevelopment as result of low amniotic fluid volumes, requiring intensive care and close monitoring. It occurs in about one in 8000 babies.

An accessory auricle is considered a developmental anomaly resulting from the persistence of a structure which variably recapitulates the normal external ear.

Megaureter is a medical anomaly whereby the ureter is abnormally . Congenital megaureter is an uncommon condition which is more common in males, may be bilateral, and is often associated with other congenital anomalies. The cause is thought to be aperistalsis of the distal ureter, leading to dilatation.

The cutoff value for megaureter is when it is wider than 6 or 7 mm.

A functional obstruction at the lower end of the ureter leads to progressive dilatation and a tendency to infection. The ureteric orifice appears normal and a ureteric catheter passes easily.

Definitive surgical treatment involves refashioning the lower end of the affected ureter so that a tunnelled reimplantation into the bladder can be done to prevent reflux.

Caudal regression syndrome or sacral agenesis (or hypoplasia of the sacrum) is a congenital disorder in which there is abnormal fetal development of the lower spine—the caudal partition of the spine.

It occurs at a rate of approximately one per 25,000 live births.

Macroglossia is uncommon, and usually occurs in children. Macroglossia has been reported to have a positive family history in 6% of cases. The National Organization of Rare Disorders lists macroglossia as a rare disease (less than 200 000 individuals in the US).

Vertebral anomalies is associated with an increased incidence of some other specific anomalies as well, together being called the VACTERL association:

- V - "Vertebral anomalies"

- A - Anal atresia

- C - Cardiovascular anomalies

- T - Tracheoesophageal fistula

- E - Esophageal atresia

- R - Renal (Kidney) and/or radial anomalies

- L - Limb defects

Splenogonadal fusion is a rare congenital malformation that results from an abnormal connection between the primitive spleen and gonad during gestation. A portion of the splenic tissue then descends with the gonad. Splenogonadal fusion has been classified into two types: continuous, where there remains a connection between the main spleen and gonad; and discontinuous, where ectopic splenic tissue is attached to the gonad, but there is no connection to the orthotopic spleen. Patients with continuous splenogonadal fusion frequently have additional congenital abnormalities, most commonly cryptorchidism.

The anomaly was first described in 1883 by Bostroem. Since then more than 150 cases of splenogonadal fusion have been documented. The condition is considered benign. A few cases of testicular neoplasm have been reported in association with splenogonadal fusion. The reported cases have occurred in patients with a history of cryptorchidism, which is associated with an elevated risk of neoplasm.

Splenogonadal fusion occurs with a male-to-female ratio of 16:1, and is seen nearly exclusively on the left side. The condition remains a diagnostic challenge, but preoperative consideration of the diagnosis may help avoid unnecessary orchiectomy. On scrotal ultrasound, ectopic splenic tissue may appear as an encapsulated homogeneous extratesticular mass, isoechoic with the normal testis. Subtle hypoechoic nodules may be present in the mass. The presence of splenic tissue may be confirmed with a technetium-99m sulfur colloid scan.

Diastematomyelia (occasionally diastomyelia) is a congenital disorder in which a part of the spinal cord is split, usually at the level of the upper lumbar vertebra.

Diastematomyelia is a rare congenital anomaly that results in the "splitting" of the spinal cord in a longitudinal (sagittal) direction. Females are affected much more commonly than males. This condition occurs in the presence of an osseous (bone), cartilaginous or fibrous septum in the central portion of the spinal canal which then produces a complete or incomplete sagittal division of the spinal cord into two hemicords. When the split does not reunite distally to the spur, the condition is referred to as a diplomyelia, or true duplication of the spinal cord.

Midline cervical clefts are a rare congenital anomaly resulting from incomplete fusion during embryogenesis of the first and second branchial arches in the ventral midline of the neck. The condition presents as a midline cutaneous defect of the anterior neck with a skin projection or sinus, or as a subcutaneous erythematous fibrous cord. Surgical excision is the preferred treatment.