Gastroenterology is one of the highest-volume procedural specialties in outpatient medicine — and one of the most billing-intensive. A colonoscopy with polypectomy, an EGD with Barrett’s ablation, an ERCP with stone removal, a capsule endoscopy study, and an anorectal manometry can all occur within a single week at a busy GI practice, each carrying distinct CPT codes, distinct documentation requirements, distinct prior authorization rules, and distinct payer policies governing how multiple procedures in the same session are reimbursed.

In 2026, gastroenterology billing changed in ways that affect virtually every GI practice. The AGA, ACG, and ASGE jointly modernized anorectal physiology testing with new bundled CPT codes that replace deleted codes used by practices for years. Endoscopic sleeve gastroplasty received its first permanent Category I CPT code. EndoFLIP expanded to ASC settings. And the perennial compliance challenge — the screening-to-diagnostic colonoscopy conversion — remains under tighter payer scrutiny than ever.

This guide covers the complete gastroenterology billing and coding framework for 2026.

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Part 1: Colonoscopy Billing — The Highest-Volume and Highest-Risk Category

The Colonoscopy CPT Code Family

Code	Description
45378	Diagnostic colonoscopy — no biopsy or therapeutic intervention
45380	Colonoscopy with biopsy, single or multiple
45381	Colonoscopy with submucosal injection
45382	Colonoscopy with control of bleeding
45384	Colonoscopy with ablation of tumor, polyp, or lesion
45385	Colonoscopy with removal of tumor, polyp, or lesion by snare technique
45386	Colonoscopy with balloon dilation
45388	Colonoscopy with ablation of lesion by ablation technique
45389	Colonoscopy with stent placement
45390	Colonoscopy with endoscopic mucosal resection (EMR)
45391	Colonoscopy with endoscopic ultrasound (EUS) examination

Screening colonoscopy codes (Medicare):

Code	Description
G0105	Colorectal cancer screening colonoscopy — high risk individual
G0121	Colorectal cancer screening colonoscopy — average risk

The Screening-to-Diagnostic Conversion

When a patient presents for a screening colonoscopy and a polyp or lesion is found and removed, the procedure converts to therapeutic. The final CPT code must reflect the procedure actually performed, not the original screening intent.

Medicare Modifier PT: For Medicare patients, when a screening colonoscopy converts to a therapeutic procedure, Modifier PT must be appended to the CPT code. This signals Medicare to apply appropriate patient cost-sharing and informs secondary coverage.

ICD-10 coding for colonoscopy:

Scenario	Correct ICD-10
Average-risk screening, no findings	Z12.11
High-risk screening (family history)	Z80.0
Screening with polyp found and removed	Z12.11 + K63.5
Diagnostic for rectal bleeding	K92.1 or K92.89
IBD surveillance	K50.90 (Crohn’s) or K51.90 (UC)

The Multiple Endoscopy Rule

When two or more colonoscopy procedures occur in the same session, Medicare reimburses the highest-valued procedure at the full rate. Each additional procedure is paid at the difference between that procedure’s rate and the base diagnostic colonoscopy rate (45378) — not at its full rate. This is not the same as the standard 50% multiple procedure reduction.

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Part 2: Upper GI Endoscopy (EGD)

Code	Description
43235	Diagnostic EGD
43239	EGD with control of bleeding
43243	EGD with injection sclerotherapy of esophageal varices
43244	EGD with band ligation of varices
43246	EGD with PEG tube placement
43249	EGD with balloon dilation of esophagus
43251	EGD with removal of polyp/lesion by snare technique
43253	EGD with radiofrequency ablation (Barrett’s — RFA)
43254	EGD with endoscopic mucosal resection (EMR)
43255	EGD with control of acute upper GI hemorrhage
43259	EGD with endoscopic ultrasound (EUS)
43270	EGD with ablation of lesion by argon plasma coagulation (APC)

Barrett’s Esophagus ICD-10 Codes

Code	Description
K22.70	Barrett’s esophagus without dysplasia
K22.710	Barrett’s esophagus with low-grade dysplasia
K22.711	Barrett’s esophagus with high-grade dysplasia

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Part 3: ERCP

Code	Description
43260	ERCP, diagnostic
43262	ERCP with sphincterotomy/papillotomy
43263	ERCP with pressure measurement
43264	ERCP with removal of calculi/debris
43265	ERCP with lithotripsy
43266	ERCP with stent placement
43267	ERCP with stent removal
43268	ERCP with dilation of biliary or pancreatic duct stricture
43274	ERCP with stent placement including pre/post-dilation
43275	ERCP with removal of existing stent
43276	ERCP with stent exchange

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Part 4: 2026 Updates — Most Significant GI Code Changes in Years

1. New Anorectal Codes — Deleted Codes Must Be Retired Immediately

Deleted January 1, 2026 — do not use:

• 91120 — Rectal sensation, tone, and compliance study
• 91122 — Rectal electrosensitivity test

New Category I codes effective January 1, 2026:

Code	Description
91124	Rectal sensation, tone, and compliance study (e.g., barostat)
91125	Anorectal manometry, with rectal sensation and rectal balloon expulsion test, when performed

91124 and 91125 cannot be reported together on the same date of service. The AGA, ACG, and ASGE developed these codes to replace the prior pair that was billed together more than 75% of the time. Documentation for 91125 must reflect all three components: anorectal manometry, rectal sensation testing, and balloon expulsion test.

2. New Permanent CPT Code 43889 — Endoscopic Sleeve Gastroplasty

CPT 43889 is the first permanent Category I code for Endoscopic Sleeve Gastroplasty, effective January 1, 2026. It covers transoral ESG using endoscopic suturing/plication including argon plasma coagulation when performed. APC is included in the code descriptor — do not bill 43270 separately for the same session. CMS exempted 43889 from standard new-code payment methodology.

3. EndoFLIP (91040) Now Approved in ASC Setting

CMS approved CPT 91040 (endoluminal functional lumen imaging probe, EndoFLIP) in the ASC setting effective January 1, 2026. Previously restricted to hospital outpatient only. GI practices with ASC capability for EndoFLIP can now bill this service at potentially higher professional fees with lower overhead.

4. ESD Available in ASC Setting

HCPCS code C9779 (endoscopic submucosal dissection) now available in ASC settings effective January 1, 2026. New Category I CPT codes for ESD are expected January 1, 2027.

5. New IB-Stim Code 64567

CPT 64567 covers periauricular placement of a non-implanted percutaneous electrical nerve field stimulator (IB-Stim) for chronic abdominal pain in patients ages 8–21 with functional abdominal pain associated with IBS or functional dyspepsia.

6. Site-of-Service Payment Shifts

The 2026 fee schedule significantly increased payment for office-based endoscopy while reducing facility-based reimbursement in ASCs and hospital outpatient departments. The -2.5% efficiency adjustment to work RVUs affects endoscopy codes.

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Part 5: Motility Testing and Capsule Endoscopy

Code	Description	2026 Status
91010	Esophageal motility study (high-resolution manometry)	Active
91035	pH electrode monitoring, 24-hour	Active
91038	Esophageal reflux test, prolonged (Bravo)	Active
91040	EndoFLIP — endoluminal functional lumen imaging	Now in ASC
91110	Capsule endoscopy, small intestine	Active
91111	Capsule endoscopy, esophagus only	Active
91112	Wireless capsule motility study (SmartPill)	Active
91120	Rectal sensation study	❌ DELETED
91122	Rectal electrosensitivity test	❌ DELETED
91124	Rectal sensation, tone, compliance study (barostat)	✅ NEW
91125	Anorectal manometry with rectal sensation + balloon expulsion	✅ NEW

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Part 6: Liver Disease and Hepatology

Code	Description
91200	Liver elastography (FibroScan) — mechanically induced shear wave
49082	Abdominal paracentesis, without imaging guidance
49083	Abdominal paracentesis, with imaging guidance

Liver disease ICD-10 codes:

Code	Description
K74.60	Unspecified cirrhosis of liver
K76.0	Fatty liver (NAFLD)
K75.81	Nonalcoholic steatohepatitis (NASH)
K70.31	Alcoholic cirrhosis with ascites
B18.2	Chronic viral hepatitis C
K72.10	Chronic hepatic failure without coma

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Part 7: Common GI ICD-10 Codes

Code	Description
K21.0	GERD with esophagitis
K21.9	GERD without esophagitis
K22.0	Achalasia
K50.90	Crohn’s disease, unspecified, without complication
K51.90	Ulcerative colitis, unspecified, without complication
K57.30	Diverticulosis of large intestine without bleeding
K57.32	Diverticulitis of large intestine without abscess, without bleeding
K58.9	Irritable bowel syndrome without diarrhea
K63.5	Polyp of colon
K92.1	Melena
K92.0	Hematemesis

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Part 8: Common Modifiers in Gastroenterology

Modifier	When to Use
PT	Medicare screening colonoscopy converted to diagnostic/therapeutic
52	Colonoscopy discontinued before completion without anesthesia
53	Discontinued procedure after anesthesia administered
59	Distinct procedural service — bypass NCCI bundling edits
26	Professional component only (capsule endoscopy interpretation)
TC	Technical component only
33	Preventive service — waives patient cost-sharing (commercial plans)
GG	Screening colorectal test converted to diagnostic (some MACs)

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Part 9: Prior Authorization — High-Risk GI Procedures

Procedure	Auth Required	Key Documentation
Capsule endoscopy (91110)	Yes — virtually all payers	Prior negative EGD and colonoscopy
ERCP (43260–43278)	Yes — most payers	Imaging supporting biliary/pancreatic pathology
EMR (45390/43254)	Yes — most payers	Prior biopsy results; lesion characteristics
ESD (C9779)	Yes — most payers	Lesion size/location; staging
ESG (43889)	Yes — most payers	BMI ≥30; prior weight loss attempts
EndoFLIP (91040)	Yes — many payers	Failed medical management; manometry results
RFA for Barrett’s (43253)	Yes — most payers	Pathology confirming dysplasia grade

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Part 10: Top Denial Reasons in GI and How to Fix Them

1. Screening-to-Diagnostic Conversion Without Modifier PT

Medicare converted screening claims without Modifier PT process incorrectly — wrong cost-sharing applied to patient.

Fix: Build a billing rule flagging therapeutic colonoscopy codes where the original order was a screening. Modifier PT required before submission.

2. Using Deleted Codes 91120 and 91122

Automatic rejection after January 1, 2026.

Fix: Remove immediately from all charge masters and templates. Replace with 91124 or 91125 as appropriate. They cannot be billed together.

3. Wrong Colonoscopy Code When Therapeutic Procedure Performed

Billing 45378 (diagnostic) when a polypectomy or biopsy was performed.

Fix: Tie CPT selection to the procedure report, not the original order.

4. ICD-10 Mismatch With Procedure Code

IBD surveillance billed with Z12.11, or therapeutic EGD billed with screening diagnosis.

Fix: Implement claim scrub for common GI ICD-to-CPT mismatches.

5. Incorrect Multiple Endoscopy Calculation

Expecting full payment for each same-session procedure and writing off the difference as a denial.

Fix: Build multiple endoscopy rule into expected payment benchmarks.

6. ESG Billed With Separate APC Code

43889 + 43270 billed together when APC is already included in 43889.

Fix: Build billing edit to remove 43270 when billed with 43889 same session.

7. Capsule Endoscopy Without Prior Auth

91110 denied — no prior auth or auth request lacked documented prior negative workup.

Fix: Require prior negative EGD and colonoscopy documentation as mandatory prerequisite for capsule endoscopy scheduling.

8. Modifier 52 vs. 53 Confusion

Using the wrong modifier for incomplete procedures.

Fix: If anesthesia was administered before discontinuation — Modifier 53. If stopped before anesthesia or without anesthesia — Modifier 52.

9. ERCP Documentation Insufficient

Billing complex ERCP code when the report does not describe each billed component.

Fix: Require procedure report review against billed ERCP code before claim submission.

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What Your GI Practice Should Do Right Now

Immediate 2026 code updates:

• Remove 91120 and 91122 from every charge master and template — replace with 91124 and 91125
• Add 43889 as permanent ESG code — remove any prior unlisted codes for this procedure
• Confirm 91040 is active in your ASC charge master if your practice performs EndoFLIP in an ASC
• Remove 43270 from ESG procedure templates — included in 43889

Colonoscopy compliance:

• Audit last 60 days of screening colonoscopy claims — confirm Modifier PT on all converted Medicare screenings
• Confirm IBD surveillance uses the active IBD code, not Z12.11

Revenue opportunities:

• If your practice has FibroScan — confirm CPT 91200 is in your charge master and being billed consistently
• Review capsule endoscopy authorization workflows — include documentation of prior negative endoscopy in every auth request
• Evaluate site-of-service strategy for endoscopy given the 2026 office-based rate increases

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Final Thoughts

Gastroenterology billing in 2026 demands precision in code selection, documentation alignment, modifier application, and understanding the multiple endoscopy reimbursement rule. The 2026 changes — new anorectal codes, permanent ESG coding, ASC expansion for EndoFLIP and ESD — require immediate charge master updates and documentation workflow adjustments.

At ClaimsXperts, gastroenterology is one of our core specialty billing areas. We work with GI practices on colonoscopy coding compliance, ERCP documentation review, 2026 code transitions, prior authorization workflows, and full-cycle revenue cycle management.

Contact us today to learn how ClaimsXperts can strengthen your gastroenterology billing operation.

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ClaimsXperts is a Revenue Cycle Management company based in Frisco, TX, serving medical practices across the United States. We specialize in medical billing, coding, and insurance credentialing for solo practitioners, group practices, and specialty clinics.