Gastroenterology Billing Cheat Sheet (2026)
Screening or diagnostic: that one classification on a colonoscopy sets both the patient's cost share and your payment, and it is where GI claims most often break. Get that wrong and you either bill the patient incorrectly or lose the screening benefit.
Quick reference for gastroenterology billers. Last updated .
Top Gastroenterology CPT Codes & 2026 Medicare Allowables
| Code | Description | Non-Facility | Facility | Total RVU |
|---|---|---|---|---|
| 43239 | Upper GI endoscopy with biopsy | $418.85 | $123.58 | 12.54 |
| 43235 | Diagnostic upper GI endoscopy (EGD) | $322.65 | $110.56 | 9.66 |
| 43248 | EGD with esophageal dilation over guide wire | $457.93 | $147.97 | 13.71 |
| 45378 | Diagnostic colonoscopy | $378.10 | $164.67 | 11.32 |
| 45380 | Colonoscopy with biopsy | $479.97 | $177.69 | 14.37 |
| 45385 | Colonoscopy with polypectomy by snare | $500.01 | $223.45 | 14.97 |
| 45390 | Colonoscopy with ablation of tumor or polyp | $290.25 | $290.25 | 8.69 |
| 91110 | Capsule endoscopy of esophagus through ileum | $802.29 | $802.29 | 24.02 |
| 99213 | Established patient office visit, low MDM | $95.19 | $57.45 | 2.85 |
National 2026 Medicare Physician Fee Schedule estimates (total RVU multiplied by the conversion factor). These are adjusted by state locality. See the per-state table on the Gastroenterology billing services page.
Modifiers That Prevent Gastroenterology Denials
A preventive screening colonoscopy on a commercial plan, so the patient cost share is waived under preventive-care rules.
A screening colonoscopy that became diagnostic when a polyp was found, on Medicare, so the deductible is waived.
Distinct lesions treated by different techniques in the same session that NCCI would otherwise bundle.
A discontinued procedure, such as an incomplete colonoscopy that did not reach the cecum, with the reason documented.
Splitting professional and technical components where the facility and physician bill separately.
A repeat procedure by the same physician with the medical reason documented.
Top Gastroenterology Denials → Quick Fix
Use the screening code (or the diagnostic code with modifier PT on Medicare, 33 on commercial) when the indication was screening. The indication, not the finding, sets the base intent.
Match the code to the technique: 45385 snare, 45384 hot biopsy or bipolar cautery, 45380 biopsy. The op note must state how the polyp was removed.
When different lesions are treated by different techniques, append modifier 59 or XS and document the separate sites and methods.
Append modifier 53 and document why the scope did not reach the cecum. Billing it as complete is a coding-accuracy denial.
Monitored anesthesia for endoscopy is separately billable by the anesthesia provider with the correct anesthesia code, not folded into the endoscopist's claim.
NCCI Bundling Watch-Outs
Code pairs from this specialty's set that carry NCCI edits. Billing both without a justified modifier triggers a bundling denial.
| Code | Bundles With | Rationale |
|---|---|---|
| 43239 | 00520 | Anesthesia service included in surgical procedure |
| 43239 | 00731 | Anesthesia service included in surgical procedure |
| 43235 | 00520 | Anesthesia service included in surgical procedure |
| 43235 | 00731 | Anesthesia service included in surgical procedure |
| 43248 | 00520 | Anesthesia service included in surgical procedure |
| 43248 | 00731 | Anesthesia service included in surgical procedure |
| 45378 | 00731 | Anesthesia service included in surgical procedure |
| 45378 | 00732 | Anesthesia service included in surgical procedure |
Documentation That Holds Up on Appeal
Screening versus diagnostic indication explicitly, since it drives the code, the modifier, and the patient cost share.
The removal technique per lesion, since the code is technique-specific.
The reason the scope did not reach the cecum, supporting modifier 53.
Each site and the technique used, supporting separate codes with modifier 59 or XS.
The method of dilation and indication, separate from the diagnostic EGD.
Revenue Gastroenterology Practices Leave on the Table
Billing a screening colonoscopy as diagnostic and triggering patient cost share that should have been waived, which generates complaints and write-offs.
Coding all polyp removals as 45385 when the technique was biopsy or hot forceps, or the reverse.
Not appending modifier 59 for distinct lesions treated by different techniques, collapsing two payable services into one.
Missing modifier 53 on incomplete procedures, which forfeits the partial payment the documentation supports.
Gastroenterology Billing FAQ
Screening or diagnostic colonoscopy, how do I decide?
By the indication the patient presented with, not what was found. A screening exam that finds and removes a polyp stays screening-based: Medicare uses modifier PT, commercial uses modifier 33, so the patient is not wrongly charged.
How do I code a polypectomy?
By technique per lesion: 45385 snare, 45384 hot biopsy or bipolar cautery, 45380 cold biopsy. The operative note has to state the method for each lesion.
Can different lesions be billed separately?
Yes, when treated by different techniques at distinct sites. Append modifier 59 or XS and document each site and method. Without it the second service bundles.
Is anesthesia for endoscopy separately billable?
Yes, by the anesthesia provider under the correct anesthesia code with time. It is not folded into the endoscopist's procedure claim.
Stop Losing Gastroenterology Revenue to Preventable Denials
Our AAPC-certified gastroenterology coders apply every rule on this sheet to your claims. Call 888-701-6090 for a free billing assessment.