Latest Guide on Gastroenterology CPT Codes (2026)

Gastroenterology CPT codes matter most when billing medical claims to get reimbursed for services. Suppose the gastroenterologist performs a screening colonoscopy and uses CPT code G0121; incorrect ICD-10 linkage (e.g., Z80.0) can lead to immediate claim denial. No matter how accurate the claim is, one incorrect code costs your practice thousands of dollars — leaving you appealing again and again.

In 2026, the major shifts occur in gastroenterology, particularly in bariatric endoscopy and anorectal physiology. If you don’t want to lose revenue anymore just because of a simple code, read this guide that delivers the updated list of gastroenterology CPT codes.

What Are Gastroenterology CPT Codes?

Gastroenterology CPT codes are established by the AMA (American Medical Association) to translate the physician’s clinical notes into standardized medical coding language.

By using these codes, health insurance companies can determine which services or treatments were delivered to the patient. It helps providers receive accurate payments without upcoding or unbundling errors — optimizing the revenue cycle.

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Overview of CPT Codes Used for Gastroenterology Billing

Here’s a quick overview of the most commonly used gastroenterology CPT codes in 2026.

Procedure Category	CPT Code	Description	When to Use
Upper GI Endoscopy (EGD)	43235	Diagnostic esophagogastroduodenoscopy	When no biopsy or intervention is performed
Upper GI Endoscopy (EGD)	43239	EGD with biopsy	When tissue samples are taken for diagnosis
Upper GI Endoscopy (EGD)	43249	EGD with balloon dilation	When dilating strictures in the esophagus
Colonoscopy	45378	Diagnostic colonoscopy	When no biopsy or treatment is performed
Colonoscopy	45380	Colonoscopy with biopsy	When tissue samples are removed
Colonoscopy	45385	Colonoscopy with snare removal	When polyps are removed using a snare
Capsule Endoscopy	91110	GI tract imaging using capsule endoscopy	When evaluating small intestine disorders
Anorectal Physiology Testing	91124	Rectal sensation, tone, and compliance testing	For evaluating rectal function
Anorectal Physiology Testing	91125	Anorectal manometry with balloon expulsion	For diagnosing constipation/incontinence
Advanced GI Procedures (2026)	43889	Endoscopic Sleeve Gastroplasty (ESG)	For non-surgical weight loss procedures

What’s New in Gastroenterology CPT Codes for 2026

By 1 January 2026, there’s a major change in gastroenterology CPT codes, especially in Endoscopic Sleeve Gastroplasty (ESG) codes. Previously, ESG procedures were reported using temporary or unlisted codes, but in 2026, a dedicated CPT code (43889) was introduced for more accurate billing. Further, the AMA deleted and revised some codes, and CMS (Centers for Medicare & Medicaid Services) updated its reimbursement policies in response to those revisions.

Newly Introduced CPT Codes (2026)

43889 – Endoscopic Sleeve Gastroplasty

The CPT codes for EGD (endoscopic sleeve gastroplasty) introduced a new code, in which 43889 being the most commonly billed.

Use CPT code 43889 when the provider performs an EGD to reduce stomach size without surgical incisions. The specialist uses an endoscopic suturing device inserted through the mouth and may also use argon plasma coagulation to reduce stomach volume by 70–80%.

Deleted & Revised CPT Code

New anorectal physiology testing codes

The anorectal physiology testing services included components such as anorectal monometry, balloon sensation test, endoanal ultrasound, and electromyography. The purpose of these tests is to diagnose the cause of constipation, incontinence, or pain, often following childbirth or neurological issues.

Before 2026, the specialist performs the above testing services and uses the CPT codes 91120 and 91122, which are replaced by the new anorectal physiology testing codes 91124 and 91125, which fall under the Gastrointestinal Imaging, Pressure Measurement and Manometric Studies category.

When to bill CPT Code 91124?

Bill CPT code 91124 when the specialist or provider performs a rectal sensation, tone and compliance. Using an instrument, such as a barostat, which indicates a balloon system, helps measure the rectal function and determine how well it relaxes and stretches.

When to bill CPT Code 91125?

If you’re performing the anorectal manometry by using the rectal sensation testing and a balloon expulsion test, then use CPT code 91125. Also, ensure that medical necessity is documented to receive full and accurate reimbursement.

Key CMS & Reimbursement Updates

The Centers for Medicare and Medicaid Services (CMS) announced updated reimbursement rates, medical necessity policies, and billing rules for 2026 to optimize the GI billing process. The major changes in reimbursement policies for gastroenterology billing and coding services include;

The payment rate increases are around 2.6% for hospitals and ambulatory departments, including outpatient settings.
CMS allows separate payments for the non-opioid pain treatments in the ASC settings.
They reduce the cost of certain services and treatments under the OPPS (Outpatient Prospective Payment System) by up to 0.5%.

Complete List of Gastroenterology CPT Codes (2026)

Upper GI Endoscopy CPT Codes

43235 – Diagnostic EGD

The CPT code 43235 is used to bill for diagnostic EGD (Esophagogastroduodenoscopy) tests that help diagnose causes of nausea, vomiting, abdominal pain, or bleeding, and to treat issues such as ulcers.

43239 – EGD with Biopsy

EGD with biopsy is used to obtain tissue samples for diagnostic evaluation, especially when abnormalities such as ulcers, inflammation, or suspected cancer are detected. To bill this service, always use CPT code 43239 for faster, more accurate reimbursement.

43249 – Balloon Dilation

Use CPT code 43249 when the provider inserts a flexible endoscope through the mouth into the esophagus, stomach and duodenum to widen the esophagus with a balloon less than 30mm in diameter.

Colonoscopy CPT Codes

45378 – Diagnostic Colonoscopy

The diagnostic colonoscopy means the provider uses a colonoscopy to examine the colon or rectum to identify abnormal mucosa or tissue (if any) and send those specimens to a laboratory for final analysis. In this case, the billing team or provider should use CPT code 45378 for faster and more accurate reimbursement.

45380 – Colonoscopy with Biopsy

The CPT code 45380 is used to look for the cause of the patient’s symptoms, which may include rectal bleeding, diarrhea, or constipation. Using a flexible colonoscope, the provider excises one or more specimens and sends them to the laboratory for a detailed diagnosis.

45385 – Colonoscopy with Snare Removal

Use CPT code 45385 when a colonoscopy involves the removal of polyps or lesions using a snare technique. This method is typically used for larger or more complex growths that require excision rather than a simple biopsy.

Capsule Endoscopy & Imaging Codes

91110 – Capsule Endoscopy

When the provider performs a capsule endoscopy for gastrointestinal tract imaging from the esophagus to the ileum, interprets the results, and prepares a report for this service, they must use CPT code 91110 for a quick payment process.

Common Modifiers Used in Gastroenterology Billing

Modifier 26 (Professional Component)

In Gastroenterology billing services, providers must use modifier 26 when the gastroenterologist performs only the evaluation and interpretation of a test, such as a colonoscopy, but doesn’t own the equipment.

Modifier TC (Technical Component)

The modifier TC is used when the gastroenterologist handles the equipment and facility costs part. It is commonly billed by the hospitals and diagnostic centers.

Modifier 59 (Distinct Procedural Service)

Modifier 59 is used to distinguish procedures, services, and treatments provided on the same day, same visit. It helps avoid bundling issues and prevents denials.

Gastroenterology Billing Challenges in 2026

In 2026, many practices that offer gastroenterology services face the biggest billing challenge due to major shifts in GI billing codes and reimbursement rates. However, there are various reasons for denials in GI billing, some of them include;

Incorrect Code Selection

Frequent changes in gastroenterology billing codes make coding difficult. Whether you’re assigning a gastroenterology ICD-10 code or procedural ones with modifiers, the incorrect code selection or mismatches lead to claim rejections.

Bundling & Unbundling Errors

Many procedures in gastroenterology are covered under a single code with strict bundling rules, such as colonoscopy with biopsy or polyp removal. If the coders use an incorrect CPT code or modifier that should be bundled under one service, the unbundling error occurs, risking the payer audits.

Documentation Gaps

In 2026, to ensure successful reimbursement of GI services, medical records should match the diagnoses and treatments provided to the patient. If the indication, findings, or techniques used during the patient care aren’t properly recorded, the payer refuses to pay.

Payer-Specific Guidelines

Every payer has its unique billing rules and reimbursement rates. If the practice fails to follow the payer-specific guidelines, the claims will be denied, regardless of how accurate they are. So, GI practices must stay updated on individual payer policies to ensure accurate billing and faster payments

Best Practices to Optimize GI Revenue Cycle

Use Updated CPT Codes

To improve the clean claim ratio, you should always use the updated CPT codes. For this, always train your billing staff and hire specialized coders who stay up to date with coding guidelines and payer changes to minimize the risk of denials and increase revenue.

Conduct Regular Audits

To optimize the revenue cycle, ensure to conduct regular medical billing audits, whether weekly or monthly. It helps you identify hidden causes, coding errors, and claims the payer won’t process, allowing your practice to resubmit them to recover lost revenue. It also enables your practice to develop new strategies to prevent such delays or denials.

Automate Billing Processes

Practices should use medical billing software and AI in the medical billing process. It helps automate the process, identify mistakes, and reduce workload — allowing your practice to focus more on patients while optimizing the revenue cycle to boost cash flow.

Partner with Expert Billing Services

The most common approach many practices take to increase revenue is to hire a specialized RCM company to outsource medical billing tasks. These medical billing companies have extensive, hands-on experience in GI billing and coding — helping practices earn more without payment delays.

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FAQs – Gastroenterology CPT Codes 2026

What is the CPT code for a colonoscopy with biopsy?

The CPT code for a colonoscopy with biopsy is 45380. It is used when a tissue sample is taken during a colonoscopy for diagnostic evaluation. This code is commonly billed for detecting abnormalities such as polyps, inflammation, or suspicious lesions.

What changed in GI CPT codes for 2026?

In 2026, several updates were introduced to improve accuracy in GI coding. New codes, such as 43889 (Endoscopic Sleeve Gastroplasty), were added, while older anorectal codes, 91120 and 91122, were deleted. They were replaced with 91124 and 91125, reflecting more detailed physiology testing and updated clinical practices.

Are old anorectal CPT codes still valid?

No, certain older anorectal CPT codes are no longer valid in 2026.

Codes such as 91120 and 91122 have been deleted and replaced with updated codes 91124 and 91125. Using outdated codes can result in claim denials and reimbursement delays.

What modifiers are used in gastroenterology billing?

Common modifiers in gastroenterology billing include 26, TC, 59, and 51. These modifiers indicate professional vs technical components, distinct procedures, or multiple services performed. Correct modifier usage is essential to avoid bundling issues and ensure proper reimbursement.

How can I reduce GI claim denials?

To reduce GI claim denials in 2026, ensure accurate CPT coding and complete documentation for every procedure. Use appropriate modifiers, verify payer-specific rules, and perform eligibility checks before services. Regular audits and staying up to date with CMS guidelines can significantly improve claim acceptance rates.

What CPT code is used for a colonoscopy?

The standard CPT code for a diagnostic colonoscopy is 45378. It is used when no biopsy or therapeutic intervention is performed during the procedure. If additional procedures are performed, different CPT codes must be used.

Can EGD and colonoscopy be billed the same day?

Yes, EGD and colonoscopy can be billed on the same day if both procedures are medically necessary. However, proper documentation and the use of modifiers such as 59 may be required to indicate distinct services. Incorrect billing can lead to bundling denials.

When to use modifier 25 in gastroenterology?

Modifier 25 is used when a significant, separately identifiable evaluation and management (E/M) service is performed on the same day as a procedure.

For example, if a patient is evaluated and then undergoes a colonoscopy, modifier 25 may be applied. Proper documentation is required to justify the additional service.

What is the difference between CPT 45378 and 45380?

CPT 45378 is used for a diagnostic colonoscopy without any intervention. CPT 45380 is used when a biopsy is performed during the procedure. The key difference is that 45380 includes tissue sampling, which impacts reimbursement and documentation requirements.

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