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Esophageal Atresia/Tracheoesophageal Fistula Overview

, MD, PhD
Department of Molecular and Human Genetics
Baylor College of Medicine
Houston, Texas

Initial Posting: ; Last Update: June 12, 2014.


Clinical characteristics.

Esophageal atresia (EA) is a developmental defect of the upper gastrointestinal tract in which the continuity between the upper and lower esophagus is lost. EA can occur with or without tracheoesophageal fistula (TEF), an abnormal connection between the trachea and the esophagus.


EA may be detected prenatally and postnatally by imaging studies. EA/TEF can be isolated (not associated with other birth defects), syndromic (associated with other birth defects comprising a specific genetic diagnosis), or non-isolated (associated with other defects, but not a specific genetic diagnosis). Diagnosis of syndromic EA/TEF is based on clinical findings with or without molecular confirmation.

Genetic counseling.

If an individual with EA/TEF has a specific genetic syndrome or an inherited or de novo chromosome abnormality, genetic counseling for that condition is indicated. Isolated EA/TEF is generally considered to be inherited in a multifactorial manner.


Treatment of manifestations: Initial postnatal intervention is aimed at minimizing the risk for aspiration pneumonia. Surgical repair consists of closure of the TEF and anastomosis of the esophageal segments. Other abnormalities are treated symptomatically.


Esophageal atresia (EA) is a developmental defect of the upper gastrointestinal tract in which the continuity between the upper and lower esophagus is lost. EA can occur with or without tracheoesophageal fistula (TEF), an abnormal connection between the trachea and the esophagus.

The following five EA/TEF configurations have been described [Clark 1999] (see Figure 1):

Figure 1.

Figure 1.

EA/TEF configurations and their frequencies

  • EA with a distal TEF, the most common (84%)
  • Isolated EA (i.e., without TEF) (8%)
  • H-type TEF with no EA (4%)
  • EA with proximal and distal TEF (3%)
  • EA with a proximal TEF (1%)

Although EA/TEF can occur as an isolated finding, large epidemiologic studies suggest that up to 60% of individuals with EA/TEF have additional anomalies [Shaw-Smith 2006].

EA/TEF can occur in the following settings:

  • Isolated. Not associated with other birth defects
  • Syndromic. Associated with other birth defects leading to a specific genetic diagnosis
  • Non-isolated. Associated with other defects, but not leading to a specific genetic diagnosis
    • VACTERL association. Non-random association of vertebral, anal, cardiac, tracheoesophageal fistula, renal, and limb defects – that occur together more often than would be expected by chance but are not known to be caused by a unifying genetic defect (i.e., a subgroup of non-isolated but not syndromic EA/TEF). Approximately 10% of infants with EA/TEF have at least two of the other defects included in VACTERL and can be said to have VACTERL association if a specific diagnosis cannot be reached [Chittmittrapap et al 1989].

Clinical Manifestations of EA/TEF

Infants with congenital forms of EA/TEF usually present shortly after birth with copious oral secretions, coughing, gagging, cyanosis, vomiting, and/or respiratory distress.

Establishing the Diagnosis of EA/TEF

EA/TEF may be suspected prenatally if ultrasound examination reveals polyhydramnios, absence of a fluid-filled stomach, a small abdomen, lower-than-expected fetal weight, and a distended esophageal pouch [Kronemer & Snyder-Warwick 2013]. Fetal MRI may be used to confirm the presence of EA/TEF [Langer et al 2001].

EA may be detected postnatally by:

  • Failure to pass a nasogastric (NG) tube and radiographs that demonstrate coiling of the NG tube in the pouch
  • Tracheal compression and deviation on plain chest radiographs
  • Absence of a gastric bubble on plain radiographs, which may suggest EA without a TEF or EA with a proximal TEF
  • Three-dimensional CT scanning [Kronemer & Snyder-Warwick 2013]

Note: Administration of barium into the esophagus followed by chest radiographs can confirm the diagnosis but is seldom required.

Differential Diagnosis of EA/TEF

Laryngotracheoesophageal cleft. Midline defect between the posterior larynx and trachea and the anterior wall of the esophagus. This entity can present prenatally with polyhydramnios and a small or absent stomach bubble and postnatally with aspiration after feeding. Laryngotracheoesophageal clefts are commonly associated with other anomalies including TEF.

Esophageal webs/rings. Circumferential partial obstruction of the esophageal lumen caused by membranous or diaphragmatic tissue that can be associated with TEF. Many cases are asymptomatic. Symptomatic esophageal webs/rings typically present with recurrent vomiting, dysphagia (solid>liquids), and sometimes aspiration. These symptoms tend to occur later in life than those caused by EA.

Esophageal stricture. A narrowing of the esophageal lumen caused by a variety of intrinsic and extrinsic disease processes. Congenital esophageal strictures typically present after the newborn period in a manner similar to that seen in esophageal webs/rings.

Esophageal diverticulum. A sack or pouch arising from the esophagus. Esophageal diverticula can be present at birth but most often arise and/or become symptomatic in adulthood, presenting with a history of dysphagia, chest pain, vomiting, and sometimes aspiration pneumonia.

Tubular esophageal duplications. Tubular channels that lie parallel to the esophagus and often connect to the main esophageal lumen or the stomach. These lesions are often asymptomatic and are most commonly identified serendipitously at autopsy. Symptoms typically result from inflammation and/or distention secondary to food entrapment and typically involve intermittent dysphagia.

Congenital short esophagus. An abnormally short esophagus accompanied by an intrathoracic location of part of the stomach. Symptoms are often present at birth and include gastroesophageal reflux and vomiting.

Tracheal agenesis/atresia. Lack of communication between the larynx and the alveoli of the lungs. This can be associated with other anomalies including TEF. Prenatal findings can include hyperechoic lungs, flattened diaphragms, oligo- or polyhydramnios, and large breathing movements. Postnatal symptoms include severe respiratory distress, cyanosis, absent cry, and failure to ventilate despite tracheal intubation.

Prevalence of EA/TEF

The incidence of EA/TEF is approximately 1:3500 [Shaw-Smith 2006].

Causes of EA/TEF

Environmental (Acquired) Causes

Although exposure to certain medications and infections during pregnancy have been proposed as possible risk factors for development of esophageal atresia/tracheoesophageal fistula (EA/TEF), no external factor has been consistently linked to the development of EA/TEF [Felix et al 2007].

Exposure to methimazole during pregnancy has been postulated to cause a specific embryopathy, which includes EA/TEF, but data supporting this association remain anecdotal [Clementi et al 1999, Di Gianantonio et al 2001].

Maternal diabetes mellitus has been suggested as a possible risk factor for development of VACTERL association [Castori et al 2008].

Heritable Causes

Chromosomal Causes

Chromosome anomalies have been reported in approximately 6%-10% of individuals with EA/TEF [Felix et al 2007].

EA/TEF is found in the following aneuploidy syndromes [Felix et al 2007]:

  • Trisomy 21 (~0.5%-1.0% of affected individuals)
  • Trisomy 18 (~25% of affected individuals)
  • Trisomy 13
  • (Mosaic) trisomy X

A review of published chromosomal deletions/duplications associated with EA/TEF reveals that they are distributed in a non-random pattern with several regions of the genome being recurrently affected [Felix et al 2007].

  • Recurrent duplications of 3p25-pter and 5q34-qter suggest that these regions may harbor one or more genes in which overexpression causes or predisposes to the development of EA/TEF.
  • Recurrent deletions of 2q37.2-qter, 4q35-qter, 5p15-pter, 6q13-q15, 14q32.3-qter, and 17q22-q23 suggest that haploinsufficiency or decreased expression of one or more genes in these regions may cause or predispose to the development of EA/TEF.
  • Recurrent deletions of 13q34-qter and 22q11 are also associated with EA/TEF but typically are associated with findings consistent with VACTERL association [Walsh et al 2001, Felix et al 2007].

Single-Gene Causes

Autosomal dominant syndromic EA/TEF (Table 1)

  • Anophthalmia-esophageal-genital (AEG) syndrome is characterized by anophthalmia/microphthalmia, EA with our without TEF, and urogenital anomalies such as cryptorchidism, hypospadias, and micropenis. Heterozygous pathogenic variants in SOX2 are causative [Williamson et al 2006] (see SOX2-Related Eye Disorders).
  • CHARGE syndrome. Although EA/TEF is not a major criterion for diagnosis of CHARGE syndrome (coloboma of the eye, heart anomaly; atresia of the choanae, retardation of mental and somatic development, genital hypoplasia, and ear abnormalities and/or hearing loss), it is present in approximately 15%-20% of infants with this disorder. Approximately 60% of individuals with CHARGE syndrome have a heterozygous pathogenic variant in CHD7 [Vissers et al 2004].
  • Feingold syndrome is characterized by variable combinations of esophageal and duodenal atresias, microcephaly, learning disabilities, syndactyly, and cardiac defects. Heterozygous pathogenic variants and whole-gene deletions of MYCN are causative [van Bokhoven et al 2005].
  • Pallister-Hall syndrome is characterized by hypothalamic hamartoma, central and postaxial polydactyly, imperforate anus, renal anomalies, bifid epiglottis, and tracheal clefts. Heterozygous pathogenic variants in GLI3 cause Pallister-Hall syndrome. A de novo heterozygous sequence variant in the N-terminal region of GLI3 (c.332T>C, p.Met111Thr) has been described in one individual with esophageal atresia and hemivertebrae [Yang et al 2014].

Table 1.

Autosomal Dominant Syndromic EA/TEF

SyndromeGeneClinical FindingsSelected OMIM Links
Anophthalmia-esophageal-genital syndromeSOX2
  • Anophthalmia/microphthalmia
  • EA/TEF
  • Urogenital anomalies
CHARGE syndromeCHD7
  • Coloboma of the eye
  • Cardiac anomalies
  • Choanal atresia
  • Intellectual disability
  • Growth retardation
  • Genital anomalies
  • Ear anomalies
  • Hearing loss
  • EA/TEF
Feingold syndromeMYCN
  • Esophageal and duodenal atresias
  • Microcephaly
  • Learning disabilities
  • Syndactyly
  • Cardiac defects
Pallister-Hall syndromeGLI3
  • Hypothalamic hamartoma
  • Central and postaxial polydactyly
  • Imperforate anus
  • Renal anomalies
  • Bifid epiglottis
  • Tracheal clefts
  • EA/TEF (rare)

Autosomal recessive syndromic EA/TEF (Table 2)

  • Fanconi anemia is characterized by bone marrow failure, an increased risk for malignancies, and a wide variety of physical abnormalities that can include short stature, abnormal skin pigmentation, radial ray defects, eye anomalies, renal anomalies, cardiac defects, abnormal ears, central nervous system anomalies, hearing loss, and developmental delay. Gastrointestinal anomalies are common and can include EA/TEF [Berrebi et al 2006]. Fifteen of the 16 Fanconi anemia complementation groups are associated with autosomal recessive inheritance. The exception is complementation group B, which has X-linked inheritance. Autosomal recessive EA/TEF has been described in individuals with biallelic pathogenic variants in FANCA, FANCC, and ERCC4.

Table 2.

Autosomal Recessive Forms of Syndromic EA/TEF

SyndromeGenesClinical FindingsSelected OMIM Links
Fanconi anemiaFANCA
  • Bone marrow failure
  • Malignancies
  • Short stature
  • Abnormal skin pigmentation
  • Radial ray defects
  • Eye anomalies
  • Renal anomalies
  • Cardiac defects
  • Abnormal ears
  • Central nervous system anomalies
  • Hearing loss
  • Developmental delay
  • Gastrointestinal anomalies including EA/TEF

X-linked syndromic EA/TEF (Table 3)

  • X-linked Opitz G/BBB syndrome is characterized by midline abnormalities including cleft lip, heart defects, hypospadias, agenesis of the corpus callosum, and laryngeal clefts. Rare individuals exhibit EA/TEF [De Falco et al 2003]. Pathogenic variants in MID1 are causative of X-linked Opitz G/BBB syndrome [Quaderi et al 1997].
  • VACTERL association with hydrocephalus (VACTERL-H) is characterized by vertebral anomalies, anal atresia, cardiac malformations, TEF, renal anomalies, limb anomalies, and hydrocephalus. Pathogenic variants in the Fanconi anemia complementation group B gene, FANCB, have been identified in males with this phenotype [Holden et al 2006].

Table 3.

X-Linked Forms of Syndromic EA/TEF

SyndromeGeneClinical FindingsSelected OMIM Links
X-linked Opitz G/BBB syndromeMID1
  • Midline abnormalities including:
  • Cleft lip
  • Laryngeal cleft
  • Heart defects
  • Hypospadias
  • Agenesis of the corpus callosum
  • EA/TEF (rare)
  • Vertebral anomalies
  • Anal atresia
  • Cardiac malformations
  • Tracheoesophageal fistula
  • Renal anomalies
  • Limb anomalies
  • Hydrocephalus

Multifactorial Inheritance

The inheritance pattern of EA/TEF for which a specific genetic diagnosis cannot be made is generally considered to be multifactorial.

Unknown Cause

It is not known in what proportion of individuals with EA/TEF the cause is unknown.

Evaluation Strategy

Once the diagnosis of esophageal atresia/tracheoesophageal fistula (EA/TEF) has been established in an individual, the following evaluations may help determine if the EA/TEF is isolated, syndromic, or non-isolated. These evaluations may also provide information that can be used in discussions of prognosis and recurrence risk counseling.

  • Family history. A three-generation family history to determine the inheritance pattern in the family and to look for findings in other relatives that could suggest a specific etiology and/or mode of inheritance
  • Physical examination to look for additional anomalies including limb defects and anal anomalies
  • Imaging studies to identify additional anomalies of the skeleton, heart, and/or kidneys
  • Testing
    • Molecular genetic testing. When a genetic syndrome is suspected, the gene(s) responsible can be tested individually or as part of a multi-gene panel (see Causes). Alternatively, exome or genome approaches can be used to identify deleterious sequence changes in genes associated with EA/TEF.
    • Array-based copy number detection assays and/or a chromosome analysis. These tests may be ordered if a specific chromosomal disorder is suspected or as a screening test for chromosomal anomalies associated with EA/TEF.
      Note: Because array-based copy number detection assays are able to detect small chromosomal deletions and duplications that are undetectable using chromosome analysis, an array-based copy number detection assay should typically be ordered unless a balanced chromosomal rearrangement or aneuploidy is suspected.

Genetic Counseling

Genetic counseling is the process of providing individuals and families with information on the nature, inheritance, and implications of genetic disorders to help them make informed medical and personal decisions. The following section deals with genetic risk assessment and the use of family history and genetic testing to clarify genetic status for family members. This section is not meant to address all personal, cultural, or ethical issues that individuals may face or to substitute for consultation with a genetics professional. —ED.

Mode of Inheritance

Esophageal atresia/tracheoesophageal fistula (EA/TEF) can occur as an isolated finding, as part of a genetic syndrome, or as part of a non-isolated (but not syndromic) set of findings.

If an affected individual is found to have an inherited or de novo chromosome abnormality, or a specific syndrome or association with EA/TEF, genetic counseling for that condition is indicated.

Nonsyndromic EA/TEF is generally considered to be inherited in a multifactorial manner.

Empiric Risks to Family Members – TEF

Most individuals with EA/TEF represent simplex cases (i.e., the only affected member of the family). A small subset of families are multiplex (i.e., two or more relatives have EA/TEF).

Sibs of a proband. For individuals with isolated EA/TEF without a clear etiology, recurrence risk for sibs is likely to be approximately 1% [Shaw-Smith 2006]. The twin concordance rate for EA/TEF is also low (~2.5%) [Robert et al 1993]. Note: No data for recurrence risks for isolated vs non-isolated EA/TEF are available.

Offspring of a proband. In individuals with EA/TEF without a clear etiology, recurrence risk to offspring for EA/TEF and/or malformations in the VACTERL association is likely to be between 2% and 4% [Shaw-Smith 2006]. Note: Since these estimates were generated by studying the offspring of individuals with both isolated and non-isolated EA/TEF, the risk to offspring in isolated cases may be lower.

Empiric Risks to Family Members – Non-Isolated EA/TEF

Recurrence risk counseling for individuals with non-isolated EA/TEF – in whom additional anomalies have been identified and for whom a specific genetic disorder is not recognized – is problematic.

Thus, counseling in this setting should be as for other multiple congenital anomaly disorders of unknown etiology. Specifically, the estimated recurrence risk to sibs is "low”; however, this estimate represents an averaging of a negligible, or very low, recurrence risk in the majority of families together with a higher recurrence risk (≤25%-50%) in the minority of families.

Related Genetic Counseling Issues

DNA banking is the storage of DNA (typically extracted from white blood cells) for possible future use. Because it is likely that testing methodology and our understanding of genes, allelic variants, and diseases will improve in the future, consideration should be given to banking DNA of affected individuals.

Prenatal Testing

If the pathogenic variant(s) have been identified in an affected family member, prenatal testing for pregnancies at increased risk may be available from a clinical laboratory that offers either testing of this gene or custom prenatal testing.

Ultrasound examination

  • Prenatal ultrasound examination of a fetus affected by EA/TEF may reveal an absent or small fetal stomach bubble in combination with maternal polyhydramnios [Houben & Curry 2008]. The diagnostic accuracy is increased if an anechoic area is present in the middle of the fetal neck because it can help differentiate EA from diseases with possible swallowing impairments [Kronemer & Snyder-Warwick 2013]. In one study of 87 fetuses with a small (n = 53) or absent stomach bubble (n = 34), the positive predictive value of an absent stomach bubble and polyhydramnios was 56% and the sensitivity of prenatal sonography in the diagnosis of EA was 42% based on the outcome of all fetuses scanned during the same period [Stringer et al 1995]. The positive predictive value is likely to be even lower among fetuses with multiple anomalies [Choudhry et al 2007].
  • The presence of a dilated blind-ending esophageal pouch on a sonogram is suggestive of EA; it is the most reliable sonographic sign indicative of EA and has been seen in cases with and without TEF [Kronemer & Snyder-Warwick 2013].
  • Polyhydramnios can be seen in a wide variety of disorders and alone is a poor indicator of EA: only one in 12 fetuses with polyhydramnios has EA [Kronemer & Snyder-Warwick 2013].
  • When EA/TEF is suspected on routine prenatal ultrasound examination:
    • A high-resolution ultrasound examination is indicated;
    • Fetal MRI should be considered to help confirm the diagnosis of EA/TEF and to evaluate for additional structural anomalies;
    • Chromosome analysis, an array-based copy number detection assay, and/or molecular testing using fetal cells/DNA should be considered.
  • All fetuses suspected of having EA/TEF should be evaluated for the presence of additional major malformations that could be part of an underlying syndrome because such malformations and/or the underlying diagnosis may significantly affect the prognosis. Involvement of a medical geneticist in the evaluation of these families can be helpful.


GeneReviews staff has selected the following disease-specific and/or umbrella support organizations and/or registries for the benefit of individuals with this disorder and their families. GeneReviews is not responsible for the information provided by other organizations. For information on selection criteria, click here.


Evaluations Following Initial Diagnosis

After an individual has been diagnosed with esophageal atresia/tracheoesophageal fistula (EA/TEF), the following evaluations should be considered as a means of identifying associated anomalies:

  • X-ray evaluation for vertebral anomalies
  • Echocardiogram
  • Renal ultrasound examination

Treatment of Manifestations

Initial postnatal intervention, aimed at minimizing the risk of aspiration pneumonia, typically includes the elimination of oral feeds, placement of a suction catheter to allow continuous drainage of secretions, and elevation of the head of the bed to minimize reflux [Clark 1999]. Intravenous (IV) glucose and fluids should be provided; supplemental oxygen should be administered as needed. When intubation cannot be avoided, a possible complication is the collection of air in the stomach, which in severe cases can only be removed by gastrostomy.

Surgical repair consists of closure of the TEF and anastomosis of the esophageal segments [Sharma & Duerksen 2012]. Surgical repair may need to be delayed in infants with low birth weight, pneumonia, or other major congenital anomalies. When surgical repair is delayed, infants may be treated with parenteral nutrition, gastrostomy tube placement, and upper pouch suctioning until they become surgical candidates.

The most common complications after surgical repair include leakage at the site of the anastomosis, recurrent fistula, structure formation, and gastroesophageal reflux [Clark 1999, Sharma & Duerksen 2012, Kronemer & Snyder-Warwick 2013].

Evaluation of Relatives at Risk

See Genetic Counseling for issues related to testing of at-risk relatives for genetic counseling purposes.

Therapies Under Investigation

Search for access to information on clinical studies for a wide range of diseases and conditions. Note: There may not be clinical trials for this disorder.


Literature Cited

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Chapter Notes

Author Notes

Author’s Web page

Revision History

  • 12 June 2014 (me) Comprehensive update posted live
  • 12 March 2009 (me) Review posted live
  • 14 October 2008 (das) Original submission
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