What Is CPT Code 45390?
CPT code 45390 is the procedure code for a colonoscopy with endoscopic mucosal resection (EMR), a technique that uses submucosal injection followed by snare resection to remove flat or sessile lesions from the colonic mucosa. It is the highest-complexity polypectomy code in the standard colonoscopy set and carries significantly higher reimbursement than snare polypectomy (45385) because EMR requires a documented lift-and-cut technique. Under the 2026 Medicare Physician Fee Schedule, 45390 reimburses approximately $321 in the office setting and approximately $698 in a facility setting before geographic adjustments.
What makes it different from 45385: 45390 requires a documented submucosal injection that lifts the lesion before snare removal. Without the documented lift, the procedure is a standard snare polypectomy billed under 45385, not 45390.
The bundling trap: CPT 45381 (submucosal injection) is bundled into 45390 with modifier indicator 0, meaning it cannot be billed separately when EMR is performed. Billing both on the same claim denies every time.
The audit risk: The OIG has identified upcoding from 45385 to 45390 as a documented compliance focus in colonoscopy billing reviews. Documentation must clearly support that EMR, not standard snare polypectomy, was performed.
What CPT Code 45390 Covers
CPT 45390 reports a flexible colonoscopy with endoscopic mucosal resection. The AMA CPT descriptor reads: ‘Colonoscopy, flexible; diagnostic, including collection of specimen(s) by brushing or washing, when performed, with endoscopic mucosal resection.’ The procedure involves injecting a solution (typically saline, sometimes with epinephrine or a viscous agent) into the submucosal layer beneath the lesion, creating a fluid cushion that lifts the lesion away from the muscularis propria, and then using a snare to resect the lifted mucosa en bloc or piecemeal.
EMR is used for flat or sessile lesions that cannot be safely removed by standard snare polypectomy alone. These are typically laterally spreading tumors, large sessile polyps (generally 20 mm or larger), or residual polyp tissue at a prior polypectomy site that requires the lift technique for safe and complete removal. The procedure carries higher clinical complexity, higher equipment cost, and higher risk of perforation or bleeding than a standard snare polypectomy, which is why it commands a higher RVU assignment and reimbursement.
In our experience matching gastroenterology providers with billing partners, the most frequent billing error on 45390 is submitting it when the operative note describes a standard snare polypectomy without a documented submucosal injection and lift. The technique must be in the note for the code to hold on audit.
What Is the Difference Between CPT 45390 and 45385?
CPT 45385 is colonoscopy with removal of tumor(s), polyp(s), or other lesion(s) by snare technique. CPT 45390 is colonoscopy with endoscopic mucosal resection. The billing distinction is the submucosal injection and lift. If the gastroenterologist injected beneath the lesion and lifted it before snare resection, the procedure is 45390. If the snare was applied directly without a submucosal lift, the procedure is 45385.
| Feature | CPT 45385 (Snare Polypectomy) | CPT 45390 (EMR) |
| Technique | Snare applied directly to polyp | Submucosal injection + lift + snare resection |
| Typical lesion | Pedunculated or small sessile polyps | Flat, sessile, or laterally spreading lesions 20mm+ |
| Submucosal injection | Not included | Required and documented |
| 2026 Medicare (office) | ~$245 | ~$321 |
| 2026 Medicare (facility) | ~$445 | ~$698 |
| 45381 bundling | Billable separately with 59 | Bundled, modifier indicator 0 |
| OIG audit focus | Standard | Documented upcoding risk from 45385 |
The revenue difference is substantial. At the facility level, 45390 pays approximately $253 more per procedure than 45385. For a GI practice performing 50 EMR cases per year, the difference between coding the procedure correctly as 45390 versus undercoding it as 45385 is roughly $12,650 in annual revenue from the physician fee alone. Conversely, billing 45390 when the documentation supports only 45385 creates audit exposure that the OIG has explicitly flagged.
CPT 45390 Bundling and NCCI Edits
The most important NCCI edit on 45390 is the bundling of CPT 45381 (colonoscopy with directed submucosal injection). Because EMR inherently includes a submucosal injection as part of the lift-and-cut technique, CMS bundles 45381 into 45390 with modifier indicator 0, meaning the bundle cannot be overridden with modifier 59. Billing 45381 alongside 45390 on the same claim will deny.
The base colonoscopy code 45378 is also bundled into 45390. If the only intervention performed during the colonoscopy is EMR, the claim carries 45390 alone. Do not bill 45378 alongside 45390 for the same session.
Additional therapeutic codes can be billed with 45390 when distinct procedures are performed at separate sites during the same session. CPT 45380 (biopsy at a different site), 45384 (hot biopsy forceps removal at a different site), and 45385 (snare polypectomy at a different site) are potentially billable alongside 45390 with modifier 59 or XS, provided the documentation supports a distinct anatomic site. For how preventive screening modifiers interact with therapeutic codes on the same colonoscopy claim, see our modifier 33 billing guide.
EMR billing is the highest-revenue colonoscopy code and the highest-audit-risk colonoscopy code. If your billing team does not know the difference between 45390 and 45385 at the documentation level, every EMR case is either underbilled or sitting in an audit queue. A billing partner with GI-specific coding expertise catches both. Gastroenterology Billing matches your practice with vetted billing companies, free.
How to Document CPT 45390 for Audit Defense
Across the billing companies we vet for GI practices, the documentation requirements for 45390 are where the most revenue is either captured or lost. These six elements must appear in the operative note.
1. Document the submucosal injection. Name the solution injected (saline, saline with epinephrine, methylene blue, Eleview, or another agent), the volume, and the injection site relative to the lesion.
2. Document the lift. State that the lesion lifted on injection. If the lesion did not lift (non-lifting sign), document that finding, as it may indicate submucosal invasion and affect the procedure approach.
3. Document the resection technique. State whether the resection was en bloc (single piece) or piecemeal (multiple pieces). If piecemeal, note the number of pieces and confirm that all visible tissue was removed.
4. Document the snare type. Specify the snare used (cold snare, hot snare, stiff snare) and the electrocautery setting if applicable. This distinguishes EMR from standard polypectomy in the operative record.
5. Document the lesion characteristics. Record the size, morphology (flat, sessile, pedunculated), location (anatomic segment of the colon), and Paris classification if used. EMR is typically applied to Paris 0-IIa, 0-IIb, or laterally spreading tumors.
6. Document completeness of resection. State whether the resection was complete, and whether the margins were inspected. If residual tissue remained, document the plan for follow-up.
One question we hear constantly from GI practice managers is why their 45390 claims get downgraded to 45385 on audit. The answer is almost always that the operative note describes a snare polypectomy with a mention of injection but does not clearly document the lift-and-cut technique that distinguishes EMR from standard polypectomy. The injection alone does not make it EMR. The documented lift is what separates the codes.
How to Bill 45390 When a Screening Colonoscopy Converts to EMR
When a screening colonoscopy identifies a lesion that requires EMR, the procedure converts from screening to therapeutic. The billing depends on the payer.
For Medicare: Bill 45390 with modifier PT. The PT modifier tells Medicare that the colonoscopy began as a screening but converted to a therapeutic procedure. Under Medicare rules, the patient’s cost-sharing is waived on the screening portion, but the patient may owe cost-sharing on the therapeutic component depending on whether the ACA colorectal cancer screening mandate applies.
For commercial payers: Bill 45390 with modifier 33. Modifier 33 identifies the service as preventive and preserves the cost-sharing waiver under the ACA, so the patient does not receive a surprise bill for what started as a covered screening colonoscopy.
Providers often come to us after patients receive unexpected bills for colonoscopies that converted from screening to therapeutic. The billing error is almost always a missing modifier PT or 33 on the therapeutic code. The procedure was billed correctly as 45390, but without the conversion modifier, the payer applied diagnostic cost-sharing instead of preventive cost-sharing, and the patient got a bill they should not have received. For the full screening-to-therapeutic conversion rules, see our 2027 Medicare GI payment changes overview.
CPT 45390 Reimbursement in 2026
Under the CY 2026 Medicare Physician Fee Schedule, CPT 45390 carries approximately 6.04 total work RVUs in the non-facility setting, with a national allowed amount of approximately $321 in the office and approximately $698 in a facility setting (ASC or HOPD) before geographic adjustments. The 2026 conversion factor is $33.4009 for non-qualifying APM participants.
Commercial payer rates for 45390 vary significantly. Published claim data shows contracted rates ranging from approximately $405 to $1,250 per procedure depending on the payer, the market, and whether the practice is billing as the professional component in a facility or as the global code in an office-based endoscopy suite. The site-of-service differential that CMS implemented in 2026, raising office-based endoscopy payments by 16% and cutting facility-based payments by 8%, makes the setting decision even more impactful for EMR cases.
For a GI practice performing 80 EMR cases per year in an office-based suite at the 2026 office rate, 45390 generates approximately $25,680 in annual professional revenue from the procedure code alone, before specimen collection, pathology, and E/M charges. The same volume in a facility generates approximately $9,600 in professional fees (with the facility billing separately). The difference in take-home physician revenue between the two settings is over $16,000 per year on EMR cases alone.
Frequently Asked Questions
What is CPT code 45390?
CPT code 45390 is the procedure code for a flexible colonoscopy with endoscopic mucosal resection (EMR). EMR involves submucosal injection to lift a flat or sessile lesion, followed by snare resection of the lifted mucosa. It is used for lesions that cannot be safely removed by standard snare polypectomy.
Can you bill 45381 with 45390?
No. CPT 45381 (submucosal injection) is bundled into 45390 with NCCI modifier indicator 0, meaning the bundle cannot be overridden. The submucosal injection is inherent to the EMR technique, so billing 45381 separately on the same claim will deny every time.
What is the difference between 45390 and 45385?
CPT 45385 is colonoscopy with standard snare polypectomy, where the snare is applied directly to the polyp. CPT 45390 is colonoscopy with EMR, which requires a documented submucosal injection and lift before snare resection. The documented lift-and-cut technique is what distinguishes the two codes.
How much does Medicare pay for CPT 45390 in 2026?
The 2026 Medicare national allowed amount for CPT 45390 is approximately $321 in the office setting and approximately $698 in a facility setting before geographic adjustments. Actual payment varies by locality and by whether the practice bills the global, professional, or technical component.
Does the OIG audit CPT 45390?
Yes. The OIG has identified upcoding from 45385 (snare polypectomy) to 45390 (EMR) as a documented compliance focus area in colonoscopy billing reviews. Documentation must clearly support that a submucosal injection and lift were performed, not just a standard snare polypectomy.
What modifier do you use when a screening colonoscopy converts to EMR?
For Medicare, append modifier PT to 45390 to indicate the colonoscopy started as a screening and converted to a therapeutic procedure. For commercial payers, append modifier 33 to preserve the preventive cost-sharing waiver under the ACA. Without the correct modifier, the patient may receive unexpected cost-sharing charges.
Next Steps
For the screening-to-therapeutic conversion rules and modifier PT vs 33 usage, see our modifier 33 billing guide.
Review the 2027 Medicare GI payment changes to see how the site-of-service differential affects EMR revenue.
Ready to stop underbilling your EMR cases? Get matched with a GI billing partner who knows the difference between 45385 and 45390 at the documentation level.
Every EMR case your practice performs is either billed as 45390 and fully reimbursed, or undercoded as 45385 and leaving $253 per case on the table. The documentation requirements are precise, the bundling rules are strict, and the OIG is watching for upcoding in the other direction. A billing partner who specializes in GI endoscopy coding handles both sides. Gastroenterology Billing matches your practice with vetted billing companies, free. All 50 states, rates starting at 2.95%.
