CPT code 45331 – Flexible sigmoidoscopy with biopsy

Key takeaways

CPT code 45331 covers a flexible sigmoidoscopy with biopsy, reported once per session however many specimens are taken.

If the scope advances beyond the splenic flexure, 45331 no longer applies, so bill a colonoscopy code such as 45378 or 45380.

Append modifier 59 when 45331 shares a date with a distinct GI procedure that an NCCI edit would bundle. Use modifier 52 for an intentionally reduced exam.

In 2026, Medicare pays about $323 for 45331 in the office and about $67 in a hospital outpatient department or ASC.

Pabau’s claims management software pre-fills the claim from the patient record and offers CPT and ICD-10-CM code lookup. It also checks that required claim fields are complete before sending.

What CPT code 45331 covers, and where it stops

CPT code 45331 is the code for a flexible sigmoidoscopy with biopsy, single or multiple, as defined by the American Medical Association. The physician passes a flexible scope through the rectum into the sigmoid colon and samples tissue at one or more sites. The exam can reach part of the descending colon, but it stays at or below the splenic flexure.

The phrase “single or multiple” matters. Whether the physician takes one specimen or six, you report 45331 once. A separate biopsy or tissue-handling charge from the same physician is unbundling, and NCCI edits will deny it.

The splenic flexure decides which code you bill

Think of the splenic flexure as a billing border. Stay at or below it and take tissue, and the claim is 45331. With no tissue taken, the right code is 45330. Advance beyond the flexure, even briefly, and the exam becomes a colonoscopy, billed as 45378 for a diagnostic exam or 45380 with biopsy.

That’s why the procedure note must record the maximum insertion depth. It’s the clinical fact that justifies the code, and the chart below maps both questions to the four codes.

Documentation that holds up when a payer audits 45331

Payer audits on flexible sigmoidoscopy claims almost always turn on what the procedure note says. Strong medical billing compliance starts with the note, long before anyone builds the claim.

The note supporting 45331 should establish five facts:

• Scope insertion depth: Record the maximum depth reached and confirm the scope stayed at or below the splenic flexure.
• Biopsy sites: Document each site sampled, how the tissue looked, and how many specimens went to pathology.
• Medical indication: State why the procedure was done, such as rectal bleeding, a change in bowel habits, or polyp surveillance.
• Specimen count: Make the pathology requisition and the procedure note agree. Mismatched counts invite denials.
• Pathology linkage: Attach the pathology report, or a pending-pathology note, so a reviewer can trace each specimen.

ICD-10 codes that support medical necessity for 45331

The diagnosis code is your medical necessity argument. A weak or mismatched ICD-10 code is one of the most common reasons 45331 claims bounce on first submission.

Modifiers for CPT code 45331, and when each one fits

Modifier choice is where experienced coders slow down. The right modifier protects payment. The wrong one, or a missing one, triggers an NCCI edit or a medical review request.

Modifiers 52 and 53 get mixed up most often. Use 52 when the physician planned a limited exam from the outset. Use 53 when the exam started but stopped early for patient safety. Swapping them sends the claim back for medical review.

What Medicare pays for CPT code 45331 in 2026

The 2026 Medicare Physician Fee Schedule pays 45331 at two rates, depending on where the procedure happens. The facility rate is lower because the hospital or ASC collects its own payment for overhead.

You can confirm both in the CMS Physician Fee Schedule lookup tool. Practices using Pabau, the practice management platform we build, can submit these claims electronically through the Claim.MD integration.

These are national figures before locality adjustment, so your payment will differ by region. Check the FastRVU 2026 RVU lookup tool before you set your fee schedule. Commercial rates vary by contract, so confirm your negotiated rate for 45331 with each payer.

After each 45331 claim pays, review the electronic remittance advice. It’s the fastest way to catch a short payment before it repeats across a billing cycle.

Medicare coverage and prior authorization

Medicare covers diagnostic flexible sigmoidoscopy under CMS coverage policies when the documented indication establishes medical necessity. Diagnostic 45331 sits apart from the screening benefits, G0121 (screening colonoscopy) and G0104 (screening flexible sigmoidoscopy). Keep these points in mind:

• The indication, such as rectal bleeding or polyp surveillance, appears in the procedure note and matches the submitted ICD-10 code.
• Screening flexible sigmoidoscopy has Medicare frequency limits, so check the applicable LCD before billing a screening exam.
• Some commercial plans, including certain UnitedHealthcare and BCBS plans, require prior authorization for elective flexible sigmoidoscopy. Verify before scheduling, not after.
• A missing authorization, where the payer requires one, is one of the most preventable 45331 denials.

How a 45331 claim moves from procedure room to payment

Here’s the path a typical office-based 45331 claim takes, and where each step can stall.

1. Scheduling: The front desk verifies eligibility and any prior authorization the plan requires.
2. Procedure note: The physician records insertion depth, each biopsy site, the specimen count, and the indication.
3. Pathology: The specimens go to the lab, which bills 88305 on its own claim.
4. Coding: The coder assigns 45331, the ICD-10 code that matches the indication, any modifier, and the place-of-service code.
5. Submission: The claim goes to the payer, usually through a clearinghouse that rejects formatting errors first.
6. Payment or denial: The remittance shows the amount paid, or a CARC reason code explaining the denial.

Steps 2 and 4 are where a short review prevents the denials listed below. When a denial does arrive, our guide to medical billing denial codes explains what each CARC code means.

Why 45331 claims get denied, and the fix for each

Most 45331 denials trace back to a handful of predictable errors. Practices with solid denial management workflows track them by CARC code, so they fix the cause upstream instead of appealing claims one at a time.

• Missing or unsupported ICD-10: The diagnosis doesn’t match the documented indication. Fix: the coder reads the procedure note for the explicit indication before assigning a code.
• Unbundling the biopsy: The performing physician bills a separate biopsy code alongside 45331. Fix: remove it, because 45331 already includes every biopsy taken. Pathology (88305) is billed separately by the pathologist.
• Billing 45330 on the same date: 45331 already includes the diagnostic exam. Fix: bill 45331 alone when a biopsy was taken.
• Same-date colonoscopy without modifier 59: 45331 and 45378 on one date trigger an NCCI edit. Fix: document distinct medical necessity and append 59.
• No prior authorization: Some commercial plans require it for elective procedures. Fix: confirm it at scheduling.
• Place-of-service mismatch: The POS code doesn’t match where the procedure happened. Fix: standardize the POS code for each site in your billing setup.
• Incomplete procedure note: Depth, biopsy sites, or pathology linkage are missing. Fix: use a structured note template that prompts for each one.

Billing 45331 with other GI codes on the same date

Same-date GI billing triggers more NCCI edit conflicts than almost any other procedure family. The AAPC’s CPT code reference and the NCCI Policy Manual list the current edit pairs. The table below covers the combinations practices ask about most.

When a patient needs both a flex sig with biopsy and a diagnostic colonoscopy on one date, document the distinct medical necessity for each. Without that note, modifier 59 won’t protect the claim.

Before you submit a 45331 claim: A quick checklist

Run through these checks before the claim leaves the practice. Each one maps to a denial reason above.

• The note records the maximum insertion depth, at or below the splenic flexure.
• Each biopsy site and the specimen count match the pathology requisition.
• The ICD-10 code matches the indication written in the note.
• 45331 appears once, with no 45330 or separate biopsy charge from the same physician.
• Any same-date colonoscopy carries modifier 59 and its own documented indication.
• The POS code matches the site: 11 for the office, 22 for hospital outpatient, 24 for an ASC.
• Prior authorization, where the plan requires it, is recorded on the claim.

How Pabau helps 45331 claims go out complete

Coding references tell your team what 45331 means. They can’t carry the code from the patient record onto the claim, and that hand-off is where errors creep in.

In Pabau’s claims management software, the claim form pre-fills the CPT code and ICD-10 diagnoses from the patient record. Built-in CPT and ICD-10-CM lookup libraries let coders confirm a code without leaving the claim. Before sending, Pabau checks that required claim fields are complete, so submitting a clean claim takes less rework.

Authorization codes are required fields on the claim before it can be sent. A missing authorization number is caught in the practice, before the claim reaches the payer.

Send 45331 claims out complete the first time

Pabau pre-fills claims from the patient record, offers CPT and ICD-10-CM code lookup, and checks required fields before you submit through Claim.MD.

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Conclusion

For 45331, the procedure note does most of the billing work. When the note proves the depth, the biopsy sites, and the indication, the code holds up in an audit.

So put your effort upstream. Fix the note template and the authorization step once, and the same denials stop repeating every month. The trade-off is a few extra fields for the physician, which costs far less than reworking claims.

Pabau supports that routine with claims pre-filled from the patient record, code lookup, required-field checks, and submission through Claim.MD. Book a demo to see how it handles your GI procedure claims.

Continue your research

Did the scope pass the splenic flexure? CPT code 45378 covers the diagnostic colonoscopy and how it differs from a flex sig.

Took a biopsy during a colonoscopy? CPT code 45380 explains how colonoscopy with biopsy is coded and paid.

Need a framework for reducing claim rejections? What is medical billing walks through the end-to-end revenue cycle process, from charge capture through payment posting.

Tracking remittance data across multiple payers? What is revenue cycle management covers how to measure and improve collection rates across a GI practice.

Want to understand clearinghouse options for GI claims? Medical claims clearinghouse explains how clearinghouses validate and route claims before they reach payers.

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