Accurate medical coding is the backbone of proper reimbursement and regulatory compliance in healthcare.
Among the numerous codes in the Current Procedural Terminology (CPT) system, CPT 43239 stands out as a frequently used code for gastrointestinal procedures.
In this comprehensive guide, we’ll break down everything you need to know about coding for esophagogastroduodenoscopy (EGD) with biopsy to ensure you’re billing correctly and maximizing reimbursement.
What is CPT Code 43239?
CPT 43239 stands for: Esophagogastroduodenoscopy, flexible, transoral; with biopsy, single or multiple.
Let’s break down this complex terminology:
- Esophago = esophagus
- Gastro = stomach
- Duodeno = duodenum (the first part of your small intestine)
- Scopy = looking inside with a scope
In simple terms, this procedure involves a physician using a flexible camera tube that enters through the mouth to examine the esophagus, stomach, and duodenum, while taking one or more tissue samples (biopsies) for analysis.
Here’s the critical coding principle to remember: Whether the physician takes one biopsy sample or ten, you bill CPT 43239 only once per session. This “single or multiple” aspect is a key feature of this code that coders must remember.
When to Use CPT 43239
You should only report code 43239 when all these criteria are met:
- Flexible scope is used (not rigid)
- The transoral approach is utilized (through the mouth, not through a surgical opening)
- At least one biopsy is performed (actual tissue removal for pathology)
- Common Clinical Scenarios
This procedure is typically performed for patients experiencing:
- A long-term GERD patient who needs Barrett’s esophagus ruled out
- Chronic stomach pain that’s not improving with standard treatment
- Unexplained bleeding in the upper GI tract
- Suspected ulcer or tumor that requires tissue confirmation
Applicable ICD-10 Codes
When coding for CPT 43239, you’ll need to link it to appropriate diagnosis codes such as:
- K20.9 – Esophagitis, unspecified
- K25.9 – Gastric ulcer, unspecified
- K31.89 – Other diseases of stomach and duodenum
- K22.2 – Esophageal obstruction
- C15.x / C16.x – Suspected cancer of the esophagus or stomach
Coding Guidelines You Can’t Ignore
This is the part where many healthcare providers make mistakes — but you won’t if you keep these in mind.
Single billing regardless of biopsy count
Consider CPT 43239 like an “all-inclusive” ticket.
Whether the provider takes one biopsy or ten, you still bill it once per session.
It doesn’t matter if samples come from the esophagus, stomach, and duodenum — the rule stays the same.
Why?
Because the CPT code covers the procedure type, not the number of samples.
Biopsy takes priority
Let’s say the doctor planned a diagnostic EGD (CPT 43235).
But once inside, they saw something suspicious and took a biopsy.
In this case, you forget about 43235 and bill 43239 instead.
A biopsy always overrides a “look-only” scope. Think of it as an upgrade — once you cut tissue, you’ve moved into a different coding category.
Multiple procedures in the same session
Sometimes, the provider doesn’t just do a biopsy. Maybe they also remove a polyp, control bleeding, or perform balloon dilation — all in one go.
If that happens, you need to check the coding rules.
If both procedures are separately reportable, you can bill them together.
But here’s the trick — you’ll likely need modifier -59 (distinct procedural service) or -XU (unusual non-overlapping service) to show they weren’t part of the same work.
Without the modifier, the second code might get denied as “bundled.”
Biopsy vs. other sampling methods
Not all sample collection is a biopsy.
If the provider only does brushings or washings (collecting cells without cutting tissue), that’s a different code.
CPT code 43239 requires cutting a piece of tissue for pathology.
If no cutting happened, don’t use 43239 — pick the correct code for the method used.
Documentation Payers Expect
Payers aren’t psychic — they only know what’s in the chart. If your documentation is missing details, you’re inviting denials.
So, documenting everything is crucial.
Anatomical sites examined
The op note should clearly state that the scope reached the esophagus, stomach, and duodenum.
This confirms the procedure was a full EGD, not just a partial.
Rationale for biopsy
As a provider, you must explain the actual reasons for the biopsy.
Examples: rule out cancer, confirm inflammation, check for ulcers, identify infection.
Without this “why,” medical necessity falls apart.
Number of biopsies
Yes, you still bill once.
But noting the number of samples adds clinical value and supports the decision to biopsy.
For example: “Two biopsies from the esophagus, one from the stomach.”
Pathology order
There must be proof that the tissue was sent to a lab.
This shows the biopsy wasn’t just taken and discarded.
It also connects the procedure to the pathology claim for cross-verification.
Medical necessity
As you know, medical necessity is the backbone of approval.
The ICD-10 codes must align with the reason for the biopsy.
If you bill 43239 for “abdominal pain, unspecified” without supporting findings, expect a denial.
Reimbursement & RVUs (2025 Data)
Let’s discuss the financial aspects of CPT 43239. According to the Medicare Physician Fee Schedule for 2025:
- RVUs: Approximately 6.74 (varies by geographic location)
- Medicare facility payment: Roughly $250–$300
- Medicare non-facility payment: Typically higher than facility payment
- Commercial payer rates: Often 15–30% higher than Medicare, depending on your contract
Remember that reimbursement rates depend on your locality and specific payer agreements. Always check your individual payer fee schedules for the most accurate information.
Let’s see CPT 43239 in action:
A doctor performs an EGD on a 54-year-old patient with persistent GERD. During the procedure, she observes inflamed patches in the lower esophagus and stomach. She takes three biopsies—two from the esophagus and one from the stomach.
Correct coding:
- CPT: 43239 (EGD with biopsy, single or multiple)
- ICD-10: K21.9 (GERD, unspecified) + K29.70 (Gastritis, unspecified)
Notice that the number of biopsy sites doesn’t change the CPT code—it’s still reported as 43239 once.
Modifiers That Might Apply
In certain situations, you may need to append a modifier to CPT 43239 to ensure proper reimbursement:
- 26: Professional component only (used when the provider only interprets the results)
- TC: Technical component only (used when only the equipment and facility costs are being billed)
- 59: Distinct procedural service (used if another unrelated endoscopic procedure is billed on the same date)
- XU: Unusual non-overlapping service (Medicare prefers this over -59 in some cases)
Understanding when to apply these modifiers is crucial for accurate billing and avoiding claim denials.
Pro Tips for Coders
Here’s how to avoid common coding headaches with CPT 43239:
- Verify the biopsy occurred: Don’t code based on assumptions—confirm tissue was removed.
- Double-check the scope type: Ensure documentation specifies a flexible scope and transoral approach.
- Read the operative note closely: Look for any additional procedures that might require separate coding.
- Match ICD-10 codes precisely: Link diagnosis codes to the exact reason for the biopsy to support medical necessity.
- Educate providers: Encourage physicians to document their findings and the rationale for each biopsy thoroughly.
Final Thoughts
CPT 43239 is straightforward once you understand the rules—but attention to detail is crucial. Focus on confirming the scope type, entry method, and biopsy documentation. Remember that whether one biopsy or ten are performed, you still bill the code only once per session. And always let the biopsy code (43239) override a diagnostic-only EGD code (43235) when both could apply.
By following these guidelines, you’ll ensure accurate coding, appropriate reimbursement, and compliance with payer requirements for EGD procedures with biopsy.
FAQS
Can I bill CPT 43239 if biopsies are taken from multiple sites?
Yes. Whether it’s one site or multiple (esophagus, stomach, duodenum), you bill 43239 once per session.
What if the provider only did brushings or washings?
That’s not 43239. This code is only for tissue biopsies. Brushings/washings have separate CPT codes.
If a diagnostic EGD was planned but a biopsy was done, which code do I use?
Always bill 43239. The biopsy procedure overrides the diagnostic-only code 43235.
Do I need modifiers with CPT 43239?
Sometimes. If another unrelated endoscopic procedure is done in the same session, you may need -59 or -XU.
What documentation is essential for billing 43239?
Procedure notes must show:
- Scope reached the esophagus, stomach, and duodenum.
- Reason for biopsy.
- Number of biopsies taken.
- Pathology order.
- Supporting ICD-10 codes.
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