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CPT 44126: Small Bowel Resection for Congenital Atresia with End-to-End Anastomosis

CPT code 44126 represents an open small bowel resection with end-to-end anastomosis for removal of a single congenital atresic (narrowed) segment. This procedure is a key surgical treatment in neonatal and pediatric general surgery when congenital intestinal atresia causes obstruction or compromised bowel function. Nationally, accurate coding for this operation affects hospital surgical case mix, inpatient payment classification, and pediatric surgical quality measurement.

Major payers discussed include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find a concise clinical context for the procedure, typical sites of service, and which payers commonly adjudicate claims for this service. The publication outlines common billing considerations and related claim elements used by payers, and it summarizes benchmarking and policy topics relevant to inpatient surgical coding and reimbursement for pediatric intestinal resections.

This overview helps clinicians, coding professionals, and policy analysts understand the procedure’s coding label and where it fits in hospital service lines, what payers to expect in national billing discussions, and which topics to review further when validating claims or evaluating payment policy updates.

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Billing Code Overview

CPT code 44126 describes an open surgical procedure in which a provider makes an abdominal incision to remove a single narrowed segment of the small intestine present from birth (congenital atresia) and restores intestinal continuity by performing end-to-end anastomosis between the remaining intestinal loops.

Service type: Surgical resection and primary anastomosis of small intestine for congenital atresia
Typical site of service: Inpatient hospital operating room and postoperative inpatient care

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CPT 44126: Small Bowel Resection for Congenital Atresia with End-to-End Anastomosis

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Billing Code Overview

Service type: Surgical resection and primary anastomosis of small intestine for congenital atresia
Typical site of service: Inpatient hospital operating room and postoperative inpatient care

Clinical & Coding Specifications

Clinical Context

A full-term neonate presents with bilious emesis, abdominal distention, and failure to pass meconium within the first 24–48 hours of life. Prenatal ultrasound had suggested intestinal dilation. Contrast study and abdominal radiographs demonstrate a single segmental obstruction consistent with jejunal or ileal atresia. After initial stabilization in the neonatal intensive care unit with fluid resuscitation, nasogastric decompression, correction of electrolyte imbalances, and intravenous broad-spectrum antibiotics, the infant is taken to the operating room for exploratory laparotomy. The surgeon makes an abdominal incision, identifies a single narrowed segment of small intestine (atretic segment), resects the diseased portion, and performs an end-to-end intestinal anastomosis to restore bowel continuity. Postoperative care includes neonatal surgical monitoring, gradual advancement of enteral feeds, pain management, and assessment for complications such as anastomotic leak, short bowel syndrome, or postoperative ileus.

Coding Specifications

Modifier	Description	When to Use
`00`	No modifier appended / unspecified	Rarely used; generally not appended when a specific modifier is appropriate
`11`	Primary procedure	When this resection and anastomosis is the principal service provided during the encounter
`22`	Increased procedural services	Use if work or complexity substantially exceeds usual (e.g., dense adhesions or anomalous anatomy requiring much additional operative time)
`52`	Reduced services	When the procedure is partially reduced or not completed as originally planned (limited resection)
`53`	Discontinued procedure	If the operation is started but terminated due to patient instability prior to completion
`59`	Distinct procedural service	When a separately identifiable procedure is performed in a different anatomic site during the same session
`62`	Two surgeons	When a qualified surgeon assists as an equally credentialed co-surgeon for complex neonatal reconstruction
`63`	Procedure performed on infants less than 4 kg	When payer requires specific modifier indicating very low birth weight status (where applicable)
`78`	Unplanned return to the operating room for a related procedure during the postoperative period	For reoperation due to complications such as anastomotic leak
`79`	(not in provided list)	Data not listed — omitted per input constraints

Taxonomy Code	Specialty	Notes
207RC0000X	Pediatric Surgery	Primary specialty performing neonatal intestinal atresia repair
2080P0200X	General Surgery	General surgeons with pediatric experience may perform the procedure in some centers
208000000X	Surgery — General	Coverage for surgeons who manage neonatal abdominal procedures
2084P0202X	Pediatric Critical Care Medicine	Perioperative management and postoperative intensive care support

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`Q41.0`	Atresia and stenosis of duodenum	Proximal intestinal atresia; relevant if the narrowed segment is duodenal and surgical repair is required
`Q41.1`	Atresia and stenosis of jejunum	Directly relevant when the resected atretic segment is within the jejunum
`Q41.2`	Atresia and stenosis of ileum	Directly relevant when the resected atretic segment is within the ileum
`P78.4`	Meconium ileus	Can present similarly with neonatal obstruction and may prompt enteric resection if complicated
`K56.2`	Volvulus (if present)	Secondary cause of focal bowel ischemia/obstruction that might necessitate resection (listed when clinically applicable)

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`44205`	Laparoscopy, surgical; enterolysis (separate procedure)	May be used if adhesiolysis is performed laparoscopically prior to or instead of open resection in older infants where laparoscopy is feasible
`44120`	Enterectomy, resection of small intestine; single resection and anastomosis	Closely related open small bowel resection code — `44126` specifies congenital atresia context; `44120` used for non-congenital resections
`49560`	Repair of inguinal hernia, complicated, with bowel resection	Example of concomitant procedures if hernia with compromised bowel is encountered (contextual; not typical for isolated atresia)
`11042`	Debridement; muscle and/or fascia (includes skin)	May be reported if a separate extensive wound debridement is required during the same operative episode
`96372`	Therapeutic, prophylactic, or diagnostic injection; subcutaneous or intramuscular	Represents postoperative medication administration in the perioperative period (billing context varies by payer)

CPT 44100: Small Intestine Biopsy via Oral Capsule

CPT-44110-OPEN-EXCISION-INTESTINAL-LESION-SINGLE-INCISION

CPT 44110: Open Excision of Intestinal Lesion(s), Single Incision

CPT-44111-INTESTINAL-LESION-EXCISION-MULTIPLE-INCISIONS

CPT 44111: Excision of Intestinal Lesions, Multiple Incisions

CPT-44120-SMALL-INTESTINE-RESECTION-PRIMARY-ANASTOMOSIS

CPT 44120: Small Intestine Resection with Primary Anastomosis

CPT-44121-ADDITIONAL-SMALL-INTESTINE-RESECTION-ANASTOMOSIS

CPT 44121: Additional Small Intestine Resection with Anastomosis

CPT-44125-SMALL-INTESTINE-RESECTION-WITH-STOMA-CREATION

CPT 44125: Small Intestine Resection with Stoma Creation

CPT-44127-SMALL-BOWEL-RESECTION-ANASTOMOSIS-INTESTINAL-ATRESIA

CPT 44127: Small-Bowel Resection with Anastomosis for Intestinal Atresia

CPT-44128-SMALL-BOWEL-RESECTION-ANASTOMOSIS-CONGENITAL-ATRESIA

CPT 44128: Small Bowel Resection and Anastomosis for Congenital Atresia

CPT-44130-INTESTINAL-ANASTOMOSIS-BOWEL-RESECTION-ANASTOMOSIS

CPT 44130: Intestinal Anastomosis, With or Without Stoma

CPT-44132-DONOR-SMALL-BOWEL-RESECTION-PRESERVATION-FOR-TRANSPLANT

CPT 44132: Donor Small Intestine Resection and Cold Preservation

Showing 1–10 of 29

Frequently Asked Questions

References

1.CPT® Codes and Descriptions. AAPC. Retrieved Jul 29, 2026.
2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Jul 29, 2026.
3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Jul 29, 2026.

Published by

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

Trek Health ingests and normalizes Transparency in Coverage data and payer policy updates to give provider organizations a clear view of how commercial reimbursement behaves across markets, payers, and services. Our platform transforms raw payer disclosures into structured intelligence that supports contract evaluation, payer negotiations, and service line strategy. By combining market benchmarks with ongoing policy visibility, Trek helps teams identify variability, risk, and opportunity in commercial reimbursement. The result is faster insight, stronger negotiating positions, and more informed financial decisions.

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Modifier	Description	When to Use
`00`	No modifier appended / unspecified	Rarely used; generally not appended when a specific modifier is appropriate
`11`	Primary procedure	When this resection and anastomosis is the principal service provided during the encounter
`22`	Increased procedural services	Use if work or complexity substantially exceeds usual (e.g., dense adhesions or anomalous anatomy requiring much additional operative time)
`52`	Reduced services	When the procedure is partially reduced or not completed as originally planned (limited resection)
`53`	Discontinued procedure	If the operation is started but terminated due to patient instability prior to completion
`59`	Distinct procedural service	When a separately identifiable procedure is performed in a different anatomic site during the same session
`62`	Two surgeons	When a qualified surgeon assists as an equally credentialed co-surgeon for complex neonatal reconstruction
`63`	Procedure performed on infants less than 4 kg	When payer requires specific modifier indicating very low birth weight status (where applicable)
`78`	Unplanned return to the operating room for a related procedure during the postoperative period	For reoperation due to complications such as anastomotic leak
`79`	(not in provided list)	Data not listed — omitted per input constraints

Taxonomy Code	Specialty	Notes
207RC0000X	Pediatric Surgery	Primary specialty performing neonatal intestinal atresia repair
2080P0200X	General Surgery	General surgeons with pediatric experience may perform the procedure in some centers
208000000X	Surgery — General	Coverage for surgeons who manage neonatal abdominal procedures
2084P0202X	Pediatric Critical Care Medicine	Perioperative management and postoperative intensive care support

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`Q41.0`	Atresia and stenosis of duodenum	Proximal intestinal atresia; relevant if the narrowed segment is duodenal and surgical repair is required
`Q41.1`	Atresia and stenosis of jejunum	Directly relevant when the resected atretic segment is within the jejunum
`Q41.2`	Atresia and stenosis of ileum	Directly relevant when the resected atretic segment is within the ileum
`P78.4`	Meconium ileus	Can present similarly with neonatal obstruction and may prompt enteric resection if complicated
`K56.2`	Volvulus (if present)	Secondary cause of focal bowel ischemia/obstruction that might necessitate resection (listed when clinically applicable)

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`44205`	Laparoscopy, surgical; enterolysis (separate procedure)	May be used if adhesiolysis is performed laparoscopically prior to or instead of open resection in older infants where laparoscopy is feasible
`44120`	Enterectomy, resection of small intestine; single resection and anastomosis	Closely related open small bowel resection code — `44126` specifies congenital atresia context; `44120` used for non-congenital resections
`49560`	Repair of inguinal hernia, complicated, with bowel resection	Example of concomitant procedures if hernia with compromised bowel is encountered (contextual; not typical for isolated atresia)
`11042`	Debridement; muscle and/or fascia (includes skin)	May be reported if a separate extensive wound debridement is required during the same operative episode
`96372`	Therapeutic, prophylactic, or diagnostic injection; subcutaneous or intramuscular	Represents postoperative medication administration in the perioperative period (billing context varies by payer)

CPT 44100: Small Intestine Biopsy via Oral Capsule

CPT-44110-OPEN-EXCISION-INTESTINAL-LESION-SINGLE-INCISION

CPT 44110: Open Excision of Intestinal Lesion(s), Single Incision

CPT-44111-INTESTINAL-LESION-EXCISION-MULTIPLE-INCISIONS

CPT 44111: Excision of Intestinal Lesions, Multiple Incisions

CPT-44120-SMALL-INTESTINE-RESECTION-PRIMARY-ANASTOMOSIS

CPT 44120: Small Intestine Resection with Primary Anastomosis

CPT-44121-ADDITIONAL-SMALL-INTESTINE-RESECTION-ANASTOMOSIS

CPT 44121: Additional Small Intestine Resection with Anastomosis

CPT-44125-SMALL-INTESTINE-RESECTION-WITH-STOMA-CREATION

CPT 44125: Small Intestine Resection with Stoma Creation

CPT-44127-SMALL-BOWEL-RESECTION-ANASTOMOSIS-INTESTINAL-ATRESIA

CPT 44127: Small-Bowel Resection with Anastomosis for Intestinal Atresia

CPT-44128-SMALL-BOWEL-RESECTION-ANASTOMOSIS-CONGENITAL-ATRESIA

CPT 44128: Small Bowel Resection and Anastomosis for Congenital Atresia

CPT-44130-INTESTINAL-ANASTOMOSIS-BOWEL-RESECTION-ANASTOMOSIS

CPT 44130: Intestinal Anastomosis, With or Without Stoma

CPT-44132-DONOR-SMALL-BOWEL-RESECTION-PRESERVATION-FOR-TRANSPLANT

CPT 44132: Donor Small Intestine Resection and Cold Preservation

Showing 1–10 of 29

Frequently Asked Questions

References

1.CPT® Codes and Descriptions. AAPC. Retrieved Jul 29, 2026.
2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Jul 29, 2026.
3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Jul 29, 2026.

Published by

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

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CPT 44126: Small Bowel Resection for Congenital Atresia with End-to-End Anastomosis

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Billing Code Overview

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Billing Code Overview

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Related Diagnoses

Related CPT Codes

Related Codes

References

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Related Diagnoses

Related CPT Codes

Related Codes

References

CPT 44126: Small Bowel Resection for Congenital Atresia with End-to-End Anastomosis

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Billing Code Overview

CPT 44126: Small Bowel Resection for Congenital Atresia with End-to-End Anastomosis

Sign up for cpt 44126 policy alerts

Billing Code Overview

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Related Diagnoses

Related CPT Codes

Related Codes

What clinical scenario and service does CPT 44126 represent?

Which modifiers are relevant when billing CPT 44126 and when are they used?

Are there related CPT codes I should consider when coding cases involving intestinal atresia repair?

Which specialties typically perform CPT 44126 and which payers are commonly involved?

What diagnosis codes are commonly associated with CPT 44126?

References

Clinical & Coding Specifications

Clinical Context

Coding Specifications

Related Diagnoses

Related CPT Codes

Related Codes

What clinical scenario and service does CPT 44126 represent?

Which modifiers are relevant when billing CPT 44126 and when are they used?

Are there related CPT codes I should consider when coding cases involving intestinal atresia repair?

Which specialties typically perform CPT 44126 and which payers are commonly involved?

What diagnosis codes are commonly associated with CPT 44126?

References