ICD-10-CM Code For Congenital Malformations Of Esophagus: Group Overview

The International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) code group Q39 includes congenital anomalies of the esophagus such as esophageal atresia and tracheoesophageal fistula that impair continuity or connection of the esophagus. These ICD-10-CM diagnosis codes are used to document newborn and pediatric presentations with feeding intolerance, aspiration risk, respiratory complications, and related surgical repairs. Accurate coding within the ICD-10-CM Q39 group supports proper claim adjudication and complete clinical documentation for appropriate reimbursement.

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ICD-10-CM Q39: Congenital Malformations Of Esophagus Overview

This group includes congenital anomalies of the esophagus such as atresia and tracheoesophageal fistula that affect swallowing and airway protection. These diagnoses target the upper gastrointestinal tract and are typically identified in neonates or infants with feeding difficulties or respiratory compromise. Accurate coding matters for appropriate clinical documentation and reimbursement because it reflects congenital severity, required interventions, and resource use.

When to Use

Use a code from this group when a congenital esophageal anomaly has been diagnosed, documented, or treated, such as during neonatal admission for feeding difficulty or surgical repair. Select the specific code that reflects the exact anatomical defect and any associated features documented by the clinician.

ICD-10-CM Codes

9 rows

ICD-10-CM Code	Description
Q39.0	Atresia of esophagus without fistula
Q39.1	Atresia of esophagus with tracheo-esophageal fistula
Q39.2	Congenital tracheo-esophageal fistula without atresia
Q39.3	Congenital stenosis and stricture of esophagus
Q39.4	Esophageal web
Q39.5	Congenital dilatation of esophagus
Q39.6	Congenital diverticulum of esophagus
Q39.8	Other congenital malformations of esophagus
Q39.9	Congenital malformation of esophagus, unspecified

DRG Codes

3 rows

DRG Code	Description
368	Major Esophageal Disorders with MCC
369	Major Esophageal Disorders with CC
370	Major Esophageal Disorders without CC/MCC

Typical Clinical Scenarios

A neonate is born with excessive oral secretions, choking on feeds and cyanotic spells during attempts at feeding; contrast esophagram in the newborn nursery demonstrates a blind-ending proximal esophageal pouch with a tracheoesophageal fistula. Surgical repair is planned during the infant’s initial hospitalization, and a congenital malformation of the esophagus diagnosis is assigned to document the anatomical anomaly causing feeding compromise. Typical codes: Q39.1, Q39.2
A toddler with a history of recurrent aspiration pneumonia and chronic cough is evaluated by pediatric gastroenterology and otolaryngology; endoscopic assessment reveals an esophageal atresia previously undiagnosed with an abnormal communication to the airway identified. The chronic respiratory and feeding symptoms prompt coding of the congenital esophageal malformation as the underlying cause of the recurrent pulmonary disease. Typical codes: Q39.1, Q39.3
An adult presents for preoperative assessment after longstanding dysphagia and prior childhood repair of an esophageal congenital anomaly; imaging and endoscopy demonstrate stricturing and dysmotility at the repair site requiring dilation and nutritional support. A congenital malformation-related diagnosis is assigned to capture the repaired congenital abnormality as the source of current complications and to guide perioperative management. Typical codes: Q39.4, Q39.6

ICD-10-CM Code For Other Congenital Malformations Of Tongue Mouth And Pharynx: Group Overview

Q40-OTHER-CONGENITAL-MALFORMATIONS-UPPER-ALIMENTARY-TRACT

ICD-10-CM Code For Other Congenital Malformations Of Upper Alimentary Tract: Group Overview

Q41-CONGENITAL-ABSENCE-ATRESIA-STENOSIS-SMALL-INTESTINE

ICD-10-CM Code For Congenital Absence, Atresia And Stenosis Of Small Intestine: Group Overview

Q42-CONGENITAL-LARGE-INTESTINE-MALFORMATIONS

ICD-10-CM Code For Congenital Absence, Atresia And Stenosis Of Large Intestine: Group Overview

Q43-OTHER-CONGENITAL-MALFORMATIONS-OF-INTESTINE

ICD-10-CM Code For Other Congenital Malformations Of Intestine: Group Overview

Q44-CONGENITAL-MALFORMATIONS-OF-GALLBLADDER

ICD-10-CM Code For Congenital Malformations Of Gallbladder, Bile Ducts And Liver: Group Overview

Q45-OTHER-CONGENITAL-MALFORMATIONS-DIGESTIVE

ICD-10-CM Code For Other Congenital Malformations Of Digestive System: Group Overview

Frequently Asked Questions

References

1.CPT® Codes and Descriptions. AAPC. Retrieved Aug 11, 2026.Maintains the CPT code set's official descriptions and guidelines, licensed from the American Medical Association, used as the definitional source for CPT codes on this page.
2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's quarterly release of HCPCS Level II codes and short/long descriptors, the source for HCPCS code definitions and update history.
3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's complete ICD-10-CM diagnosis code list, used to cross-reference diagnosis codes associated with this procedure or service.

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When to Use

ICD-10-CM Codes

9 rows

ICD-10-CM Code	Description
Q39.0	Atresia of esophagus without fistula
Q39.1	Atresia of esophagus with tracheo-esophageal fistula
Q39.2	Congenital tracheo-esophageal fistula without atresia
Q39.3	Congenital stenosis and stricture of esophagus
Q39.4	Esophageal web
Q39.5	Congenital dilatation of esophagus
Q39.6	Congenital diverticulum of esophagus
Q39.8	Other congenital malformations of esophagus
Q39.9	Congenital malformation of esophagus, unspecified

DRG Codes

3 rows

DRG Code	Description
368	Major Esophageal Disorders with MCC
369	Major Esophageal Disorders with CC
370	Major Esophageal Disorders without CC/MCC

Typical Clinical Scenarios

A neonate is born with excessive oral secretions, choking on feeds and cyanotic spells during attempts at feeding; contrast esophagram in the newborn nursery demonstrates a blind-ending proximal esophageal pouch with a tracheoesophageal fistula. Surgical repair is planned during the infant’s initial hospitalization, and a congenital malformation of the esophagus diagnosis is assigned to document the anatomical anomaly causing feeding compromise. Typical codes: Q39.1, Q39.2
A toddler with a history of recurrent aspiration pneumonia and chronic cough is evaluated by pediatric gastroenterology and otolaryngology; endoscopic assessment reveals an esophageal atresia previously undiagnosed with an abnormal communication to the airway identified. The chronic respiratory and feeding symptoms prompt coding of the congenital esophageal malformation as the underlying cause of the recurrent pulmonary disease. Typical codes: Q39.1, Q39.3
An adult presents for preoperative assessment after longstanding dysphagia and prior childhood repair of an esophageal congenital anomaly; imaging and endoscopy demonstrate stricturing and dysmotility at the repair site requiring dilation and nutritional support. A congenital malformation-related diagnosis is assigned to capture the repaired congenital abnormality as the source of current complications and to guide perioperative management. Typical codes: Q39.4, Q39.6

ICD-10-CM Code For Other Congenital Malformations Of Tongue Mouth And Pharynx: Group Overview

Q40-OTHER-CONGENITAL-MALFORMATIONS-UPPER-ALIMENTARY-TRACT

ICD-10-CM Code For Other Congenital Malformations Of Upper Alimentary Tract: Group Overview

Q41-CONGENITAL-ABSENCE-ATRESIA-STENOSIS-SMALL-INTESTINE

ICD-10-CM Code For Congenital Absence, Atresia And Stenosis Of Small Intestine: Group Overview

Q42-CONGENITAL-LARGE-INTESTINE-MALFORMATIONS

ICD-10-CM Code For Congenital Absence, Atresia And Stenosis Of Large Intestine: Group Overview

Q43-OTHER-CONGENITAL-MALFORMATIONS-OF-INTESTINE

ICD-10-CM Code For Other Congenital Malformations Of Intestine: Group Overview

Q44-CONGENITAL-MALFORMATIONS-OF-GALLBLADDER

ICD-10-CM Code For Congenital Malformations Of Gallbladder, Bile Ducts And Liver: Group Overview

Q45-OTHER-CONGENITAL-MALFORMATIONS-DIGESTIVE

ICD-10-CM Code For Other Congenital Malformations Of Digestive System: Group Overview

Frequently Asked Questions

References

1.CPT® Codes and Descriptions. AAPC. Retrieved Aug 11, 2026.Maintains the CPT code set's official descriptions and guidelines, licensed from the American Medical Association, used as the definitional source for CPT codes on this page.
2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's quarterly release of HCPCS Level II codes and short/long descriptors, the source for HCPCS code definitions and update history.
3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's complete ICD-10-CM diagnosis code list, used to cross-reference diagnosis codes associated with this procedure or service.

Published by

Trek Health powers OpenPayer with a leading commercial payer intelligence platform, seamlessly converting fragmented payer data into actionable insights for provider organizations.

ICD-10-CM Code For Congenital Malformations Of Esophagus: Group Overview

Sign up for ICD-10-CM Code For Congenital Malformations Of Esophagus: Group Overview policy alerts

ICD-10-CM Q39: Congenital Malformations Of Esophagus Overview

ICD-10-CM Code For Congenital Malformations Of Esophagus: Group Overview

Sign up for ICD-10-CM Code For Congenital Malformations Of Esophagus: Group Overview policy alerts

ICD-10-CM Q39: Congenital Malformations Of Esophagus Overview

When to Use

ICD-10-CM Codes

DRG Codes

Typical Clinical Scenarios

Related Codes

References

When to Use

ICD-10-CM Codes

DRG Codes

Typical Clinical Scenarios

Related Codes

References

ICD-10-CM Code For Congenital Malformations Of Esophagus: Group Overview

Sign up for ICD-10-CM Code For Congenital Malformations Of Esophagus: Group Overview policy alerts

ICD-10-CM Q39: Congenital Malformations Of Esophagus Overview

ICD-10-CM Code For Congenital Malformations Of Esophagus: Group Overview

Sign up for ICD-10-CM Code For Congenital Malformations Of Esophagus: Group Overview policy alerts

ICD-10-CM Q39: Congenital Malformations Of Esophagus Overview

When to Use

ICD-10-CM Codes

DRG Codes

Typical Clinical Scenarios

Related Codes

What conditions are included in the ICD-10-CM Q39 group?

Which specific ICD-10-CM codes are listed under Q39?

How does accurate coding within Q39 affect reimbursement?

In what patient population are Q39 diagnoses typically identified?

Which related DRGs are associated with major esophageal disorders linked to Q39 codes?

References

When to Use

ICD-10-CM Codes

DRG Codes

Typical Clinical Scenarios

Related Codes

What conditions are included in the ICD-10-CM Q39 group?

Which specific ICD-10-CM codes are listed under Q39?

How does accurate coding within Q39 affect reimbursement?

In what patient population are Q39 diagnoses typically identified?

Which related DRGs are associated with major esophageal disorders linked to Q39 codes?

References