Commonly Used CPT Codes in Gastroenterology

Last Updated on September 16, 2025

Gastroenterology is one of those specialties where the codes don’t change much, but the way they’re used and how often they appear does. 

In 2025, GI coders are seeing certain CPT codes show up more than ever, while others are getting flagged for bundling or documentation issues.

This article outlines the most frequently used GI CPT codes this year, not based on textbooks, but based on real usage, payer data, and forum chatter. It’s designed for coders who work in the GI space every day and need a practical list to reference or audit against.

What Are GI Coding Procedures?

GI coding is all about assigning the right CPT codes to the procedures done in gastroenterology. That includes things like scopes, biopsies, polyp removals, stents, and capsule studies. Most of the work is around upper and lower GI, EGDs, colonoscopies, and now more capsule cases showing up too.

Each procedure has its own quirks. Some codes include dilation or guidewire use, some need a modifier, and some get flagged if the op note isn’t detailed enough. It’s not just about what was done, but how it was done, and how it’s written up.

At the end of the day, GI coding isn’t complicated, but it’s picky. Knowing the codes is one thing. Knowing how payers treat them is what keeps claims clean.

CPT Code Trends: What the Numbers Show

Recent data from UnitedHealthcare’s 2024 endoscopy coding guide, as well as commercial claims data trends released in early 2025, show that procedures like diagnostic EGDs, colonoscopies with biopsy, and snare polypectomies are consistently in the top tier of billed services.

For Example:

• CPT 43239 (EGD with biopsy) remains one of the most billed codes in GI, ranking in the top 10 for GI outpatient claims across major payers.
• 45380 (colonoscopy with biopsy) and 45385 (colonoscopy with snare removal) continue to be among the highest-volume colonoscopy codes used in both hospital and ambulatory settings.
• Use of capsule endoscopy codes (91110 and 91113) has increased by nearly 9% year-over-year, according to Medicare Part B utilization reports.

These aren’t just popular, they’re also the ones most likely to cause denials when documentation doesn’t line up. That’s where coders are running into issues.

Most Common GI CPT Codes used

These aren’t just the usual codes from training manuals,  they’re the ones actually being billed every day in GI practices across the U.S. From diagnostic scopes to therapeutic interventions, this list reflects real-world frequency and how coders are adapting to documentation and payer changes.

Upper GI Procedures (EGD & Esophagoscopy)

• 43235 – EGD, diagnostic, no biopsy
  Used for basic upper GI scoping. Still appears often in workups for GERD, abdominal pain, or unexplained nausea. Watch for confusion with 43239, coders report denials when documentation doesn’t match.
• 43239 – EGD with biopsy
  A workhorse code. Tissue sampling is extremely common in upper GI cases. Document the biopsy location and reason clearly, this code is now routinely audited.
• 43251 – EGD with removal of lesion via snare
  Use this when removing polyps or other lesions with a snare tool. Not as frequent as 43239 but increasingly seen in therapeutic scoping.
• 43266 – EGD with endoscopic stent placement
  Growing in cases involving strictures or tumors. Includes pre- and post-dilation, don’t unbundle unless justified.
• 43254 – EGD with mucosal resection (EMR)
  More outpatient centers are now equipped for EMR, especially for early GI cancer removal or large polyp resections.

Colonoscopy Codes

• 45378 – Diagnostic colonoscopy (no biopsy or intervention)
  Used when no abnormality is found, and no tissue is taken. Coders often discuss this code in relation to screening vs. diagnostic billing, modifiers matter here.
• 45380 – Colonoscopy with biopsy
  Extremely common. Used in IBS/IBD workups, abnormal screening follow-ups, and cases of chronic diarrhea or bleeding.
• 45385 – Colonoscopy with snare removal of lesion/polyp
  A high-volume code. Seen in nearly every GI practice. Requires clear documentation of the snare technique, some payers now want photos in the EMR.
• 45390 – Colonoscopy with EMR
  This is used for larger or sessile lesions. Becoming more common in 2025 as EMR tech becomes more accessible.
• 45398 – Colonoscopy with band ligation
  Less frequently used, but important in hemorrhoid treatment or vascular lesion control.

Through Stoma Colonoscopies (Less Common)

These are less common but essential for patients with colostomies or surgical diversions. Coders should double-check op notes and body part terminology to use these accurately.

• 44388 – Diagnostic colonoscopy through stoma
• 44389 – With biopsy
• 44394 – With snare removal
• 44402 – With stent placement

Capsule Endoscopy (Small Bowel / Colon)

As of 2025, more payers are covering capsule endoscopies, especially when traditional scopes are incomplete or contraindicated. Coders have reported that pre-auth is increasingly required for these.

• 91110 – Capsule endoscopy, esophagus to ileum
• 91113 – Capsule endoscopy, colon

What Coding Experts Are Talking About

Coders across the industry are seeing more denials for things that used to pass through easily.

At AnnexMed, coding teams have flagged a noticeable uptick in payer pushback, especially around vague documentation and bundled services. These aren’t isolated issues, they’re part of broader trends showing up in forums, audits, and day-to-day billing.

One of our senior coders shared:

“For one of our clients we observed more frequent denials for 43239 when biopsy purpose wasn’t clear, especially in Medicare Advantage claims. We also found out that another private payer now requires photo evidence in EMR for 45385 to prove snare use. These incidences reflect a growing trend: payers want specifics.”

And we are not alone. Here’s what coders across the field are talking about in 2025:

• Bundling: Codes like 43266 (stent) and 45390 (EMR) include dilation and guidewire placement. Some coders are seeing denials for reporting those separately.
• Pre-auth requirements: Increasing, especially for advanced scopes, stents, and capsule endoscopies.
• Modifier confusion: Coders often debate when to use modifier 33 for screening colonoscopies that become diagnostic. Misuse leads to denial.
• Documentation pressure: Payers now want precise descriptions, not just “polyp removed,” but how, where, and what size.

Top GI CPT Codes Used In 2025

CPT Code	Description	Note
43239	EGD with biopsy	One of the top 10 GI CPT codes in 2024
45380	Colonoscopy with biopsy	High usage in IBD and chronic GI cases
45385	Colonoscopy with snare	Frequently used, but heavily audited
43266	EGD with stent	Includes dilation – bundling risk
91110	Capsule endoscopy (small bowel)	Usage up 9% YoY

The CPT codes themselves haven’t drastically changed, but how they’re interpreted, reimbursed, and denied has. Coders working in gastroenterology in 2025 need to be:

• Vigilant with documentation
• Updated on payer-specific guidance
• Mindful of pre-auth requirements
• Aware of bundling edits

Having a go-to list of common codes helps, but pairing it with real-world awareness is what keeps denials low and revenue steady.