According to the American Medical Association (AMA) CPT® 2026 guidelines, CPT Code 43239 describes an esophagogastroduodenoscopy (EGD) with biopsy.
The Centers for Medicare & Medicaid Services (CMS) 2025 Outpatient Prospective Payment System focuses on obtaining accurate documentation of the biopsy site and procedure details. It is also linked to clinical symptoms to confirm medical necessity and support compliant billing.
This article provides a complete and evidence-based overview of CPT Code 43239, including its description, clinical indications, modifiers, billing rules, etc.
CPT Code 43239 Description
CPT Code 43239 involves inserting a flexible endoscope through the mouth to closely examine the upper gastrointestinal tract. The primary area of focus is the esophagus, stomach, and duodenum. During the entire process, the physician performs one or more biopsies as medically indicated.
Scenarios Where CPT Code 43239 Applies
Acid Reflux & GERD
CPT Code 43239 is most of the time used to examine and evaluate gastroesophageal reflux disease (GERD). This procedure helps in assessing the extent of mucosal inflammation, erosions, or ulceration caused by acid reflux.
Pairing CPT 43239 with ICD-10 code K21.9 (GERD without esophagitis) supports medical necessity and aligns with AMA CPT® procedural reporting standards.
Barrett’s Esophagus
In cases where the medical provider might suspect Barrett’s esophagus, CPT Code 43239 is used to get biopsy samples from the distal esophagus to detect intestinal metaplasia or dysplasia.
The American College of Gastroenterology (ACG) recommends endoscopic biopsies at regular intervals for patients with confirmed Barrett’s changes. Coders must be vigilant while taking the operative note that it identifies the site and number of biopsies. The relevant ICD-10 code is K22.9 (unspecified esophageal disease).
Peptic Ulcers
CPT Code 43239 applies when biopsies are performed to confirm or assess gastric or duodenal ulcers. This procedure allows detection of Helicobacter pylori infection, mucosal inflammation, or neoplastic changes. The corresponding ICD-10 code is K29.00 (acute gastritis without bleeding).
Celiac Disease
CPT Code 43239 is used when there is a suspicion of celiac disease in any case. The American Gastroenterological Association (AGA) recommends sampling from multiple duodenal sites for diagnostic accuracy. Clinical notes must specify “celiac evaluation” and the number of biopsies taken. ICD-10 code K31.89 (other diseases of the stomach and duodenum) is the appropriate code for this disease.
Crohn’s Disease
CPT Code 43239 is also used when patients are evaluated for upper gastrointestinal involvement for Crohn’s disease. Endoscopy allows for biopsy of affected stomach lesions, esophagus, or duodenum and assessment of mucosal inflammation or granulomatous changes. Ideally, ICD-10 linkage is K31.89 or K22.9, depending on biopsy site.
Common Modifiers Used with CPT Code 43239
Modifier 51
CPT 43239 is performed in combination with another endoscopic procedure during the same session. It indicates multiple procedures by the same provider. Documentation must differentiate each service and justify the need for both. Payers may apply multiple procedure reductions when Modifier 51 is added.
Modifier 53
This modifier is applied when EGD with biopsy is started but not completed, for safety or unforeseen complications. The operative note should explain why the procedure could not be completed and what portion was performed. Correct use of Modifier 53 ensures transparent reporting and prevents overbilling.
Modifier 59
Modifier 59 indicates a procedural service that was distinct and independent of a procedure reported by a separate endoscopic code. For example, a separate biopsy was performed at another anatomic site. The use of Modifier 59 declares that the procedures were both medically necessary, distinct, and prevent bundling of the codes under NCCI edits.
Modifier XE
Modifier XE indicates the procedure occurred during a completely separate encounter on the same day. This modifier is appropriate for documentation outlining the timing and rationale for completion of a separate procedure. The XE modifier replaces Modifier 59 when payer-specific policies mandate the use of the X-modifier subset of modifiers, and clarity is required.
Modifier XP
Modifier XP applies to a different practitioner when the procedure was performed on the same day as another practitioner. The XP modifier was developed to delineate between healthcare providers and properly differentiate billing. Documentation must contain each provider’s name as well as specify distinct responsibility for performing the procedure in order to justify appropriate use of the X-modifier.
CPT Code 43239 Billing & Reimbursement Guidelines
Provide Proper Documentation
Ideally, the detailed procedure notes must include the scope entry route, areas visualized, biopsy locations, and histologic intent. Many denials come from missing biopsy detail, missing biopsy clarification, or not consistently providing indications. Link each biopsy sample to the associated pathology report for medical necessity.
Pair with the Correct Diagnostic Codes
| ICD-10 Code | Description |
| K21.9 | Gastroesophageal reflux disease without esophagitis |
| K22.9 | Unspecified disease of the esophagus |
| K29.00 | Acute gastritis without bleeding |
| K31.89 | Other diseases of the stomach and duodenum |
| C15.9 | Malignant neoplasm of the esophagus, unspecified |
Follow Payer Guidelines
Always review the Medicare Local Coverage Determinations (LCDs) and National Coverage Determinations (NCDs) for the endoscopy procedures. Many payers are asking for prior justification of the biopsy and documentation of their endoscopy findings in the record. If you are submitting a claim for a biopsy, you should always include the pathology report and operative note.
Add Correct Modifiers
Use modifiers 51, 59, XE, or XP only with distinct procedural circumstances. You should always avoid the routine use of a modifier without clear justification; this may trigger a payer audit.
Comparing CPT 43239 with Other EGD Codes
CPT 43239 vs. 43235, 43250, 43251, 43255
| CPT Code | Official CPT Description | Documentation & Billing Notes |
| 43235 | Esophagogastroduodenoscopy, flexible, transoral; diagnostic, with or without collection of specimens(s) by brushing or washing (separate procedure) | Should only be reported when no biopsy or therapeutic procedure is performed. If a biopsy is taken, code as 43239. Do not report with other EGD codes unless a distinctly separate service. |
| 43239 | Esophagogastroduodenoscopy, flexible, transoral; with biopsy, single or multiple | Must document biopsy site(s), clinical indication, and pathology correlation. Do not report multiple 43239 codes for separate biopsies, use once per session. |
43250 | Esophagogastroduodenoscopy, flexible, transoral; with removal of lesion(s), tumor(s), polyp(s), or other tissue by snare technique | The pathology intent is therapeutic, not diagnostic. Document location, size, and method of removal. Append Modifier 59 if performed with 43239 for separate lesions. |
| 43251 | Esophagogastroduodenoscopy, flexible, transoral; with removal of tumor(s), polyp(s), or other lesion(s) by hot biopsy forceps | Document the energy modality used and lesion details. Avoid unbundling with 43239 unless a biopsy from a different site is justified. Use Modifier 59 when medically supported. |
| 43255 | Esophagogastroduodenoscopy, flexible, transoral; with control of bleeding, any method | Documentation must specify the bleeding source, the control method, and success of hemostasis. Should not be reported with 43239 unless a separate and distinct pathology justifies both. |
Source: Official CPT® code descriptions and procedural guidance adapted from the AAPC CPT® Code Reference for 43235–43255, based on the American Medical Association (AMA) CPT® 2026 code set and current gastroenterology billing standards.
Common Claim Denial Reasons for CPT Code 43239
CPT Code 43239 is one of the most commonly reported and, as a result, one of the most frequently audited codes for upper GI endoscopy. Denials frequently arise due to gaps in documentation and errors in both coding and with payers. Being aware of these denials can help ensure correct reimbursement and medical billing compliance.
Common Denial Triggers
- Missing or Incomplete Procedure Documentation
Failing to address the anatomical sites visualized, locations of biopsies, or visualizing endoscopy findings is sure to get a denial. - Lack of Pathology Report Linkage
Missing or inadequate pathology correlation is one of the most common reasons for denial regarding endoscopy biopsy CPT codes. - Unjustified Medical Necessity or Incorrect ICD-10 Pairing
Using an ICD-10 diagnosis not aligned with the documented indication (e.g., nonspecific reflux without GERD) can cause payer rejection. - Incorrect Modifier Application or Duplicate Billing
Reporting multiple 43239 codes within one session or failing to apply modifiers 59, 51, or XE appropriately can trigger NCCI edit conflicts. - Failure to Follow Payer-Specific Endoscopy Coverage Policies
Every payer has their own criteria for coverage of upper GI endoscopy.
Prevention Strategy:
Conduct quarterly compliance audits, implement claim scrubber tools, and verify all modifier and ICD-10 code combinations before submission. Maintaining alignment with CPT® procedural rules and CMS billing guidelines for CPT 43239 ensures long-term reimbursement accuracy and audit readiness.
Conclusion
Nexus io has an expert team of billers and coders who specialize in addressing underpayments at the CPT code level, including CPT 43239 and other endoscopy biopsy codes. Nexus io assists healthcare organizations in identifying missed reimbursements and payer underpayments, automating compliance checks for gastroenterology billing services, and ensuring medical billing accuracy across all payer networks.
Scheduling a Nexus io demo today can help healthcare organizations discover how real-time analytics improve billing guidelines for CPT 43239, reduce audit risk, and enhance overall medical billing compliance. Optimize your gastroenterology billing workflow with automated CPT-level accuracy and payer compliance.
