Every CO 97 denial that gets caught before submission costs nothing. The same denial caught after submission costs an average rework fee, plus the time to research the NCCI pair, fix the modifier, and resubmit. The fix for that gap already exists in most practice management systems and clearinghouses; it’s just often sitting turned off, set to a lower sensitivity than it should be, or never configured for the specific code pairs that matter to your practice.
This guide covers what NCCI edit checking actually does at the scrubbing level, the general setup pattern across major PM platforms and clearinghouses, and how to confirm it’s actually catching what it should.
Key Takeaways
- NCCI edit checking compares the codes on a claim against the CMS Procedure-to-Procedure (PTP) edit table before the claim transmits, flagging bundled pairs so they can be fixed pre-submission.
- Most major PM systems and clearinghouses include this as a built-in scrubbing rule, but it isn’t always enabled by default, and the edit tables need quarterly updates to stay current.
- Turning it on isn’t enough by itself. The scrubber needs to be configured to actually stop or flag the claim, not just log a warning that gets ignored.
- Exact menu paths and setting names vary by platform and by your specific account configuration, so treat the steps below as a general pattern to follow, and confirm exact navigation with your platform’s support team or documentation.
What NCCI Edit Checking Actually Does
CMS publishes the Procedure-to-Procedure (PTP) edit table quarterly, listing which CPT code combinations are bundled (Column 1/Column 2 pairs) and whether a modifier indicator allows an override. An NCCI scrubbing rule, whether built into your PM system or running at the clearinghouse level, checks every outgoing claim against that table before it transmits to the payer.
When the scrubber finds a bundled pair without an appropriate modifier, it should do one of two things, depending on how it’s configured:
- Hard stop: block the claim from transmitting until the issue is resolved or manually overridden.
- Soft flag: let the claim through but surface a warning for the biller or coder to review.
A hard stop catches more denials but can slow down claim volume if it’s overly aggressive. A soft flag is faster but only works if someone is actually reviewing the warnings rather than clicking past them. Most practices land somewhere in between: hard stops for indicator “0” (no override possible) pairs, and soft flags for indicator “1” pairs where a modifier might legitimately apply.
The General Setup Pattern
While the exact screens differ by platform, enabling NCCI scrubbing generally follows the same sequence:
Step 1: Locate the Claim Scrubbing or Edit Rules Settings
This is usually under a billing, claims, or clearinghouse settings menu, sometimes labeled “claim edits,” “scrubbing rules,” or “pre-submission validation.” If you’re not finding it, check whether your account is connected through a separate clearinghouse rather than the PM system’s native claims engine; in that case, the setting often lives on the clearinghouse side, not inside the PM software itself.
Step 2: Confirm NCCI/CCI Edits Are Included in the Active Rule Set
Some platforms bundle NCCI checking automatically into a broader “claim scrubbing” feature; others list it as a separate, optional rule set that needs to be explicitly turned on. Look for terminology like “NCCI,” “CCI edits,” “Procedure-to-Procedure edits,” or “bundling edits.”
Step 3: Set the Edit Behavior
Decide whether flagged claims should hard-stop or soft-flag, if your platform gives you that choice. If it doesn’t, confirm which behavior is the default so your team knows what to expect.
Step 4: Verify the Edit Table Version
NCCI PTP edits update quarterly. Confirm whether your platform or clearinghouse updates its edit table automatically or requires a manual update. A scrubber running on an outdated edit table will miss newly bundled pairs and may also flag pairs that have since been removed from the bundling list.
Step 5: Test With a Known Bundled Pair
Before rolling this out across your billing team, run a test claim with a code pair you already know is bundled (one from your own denial history is ideal) and confirm the scrubber actually catches it. This is the step most practices skip, and it’s the only way to know the setting is actually working rather than just turned on.
Step 6: Roll Out and Monitor
Once confirmed, communicate the change to your coding and billing team, and monitor your CO 97 denial volume over the following weeks to confirm it’s actually dropping. If it isn’t moving, the edit rule may be misconfigured, or the edit table may not be current.
Notes by Platform Category
Major PM systems and clearinghouses, including platforms like AdvancedMD, athenahealth, Kareo, and eClinicalWorks, generally include some form of NCCI or CCI edit checking as part of their claim scrubbing toolset. Where the setting lives, what it’s called, and how granular the controls are varies by platform, by your specific account tier, and by whether you’re submitting claims through the PM system’s native clearinghouse connection or a separate third-party clearinghouse layered on top.
Because these settings and menu structures change with platform updates, the most reliable path is to search your platform’s current help documentation for “NCCI edits” or “CCI edits,” or contact your platform’s support team directly and ask specifically whether NCCI PTP edit checking is active on your account and how the edit table is kept current.
Why This Step Gets Skipped
In practices that haven’t configured this, it’s rarely a decision not to. More often, the scrubbing rule was left at a default setting during initial onboarding and never revisited, or the practice switched clearinghouses or PM platforms at some point and the setting didn’t carry over. Periodically auditing your scrubbing configuration, not just assuming it’s been handled since go-live, is worth adding to a quarterly billing operations checklist.
Frequently Asked Questions About NCCI Scrubbing Setup
Is NCCI edit checking the same as general claim scrubbing?
Not exactly. General claim scrubbing typically checks for formatting errors, missing required fields, and basic payer-specific rules. NCCI edit checking is a specific subset that compares billed code combinations against the CMS PTP bundling table. Some platforms include NCCI checking automatically within general scrubbing; others require it to be enabled separately.
Does enabling NCCI scrubbing slow down claim submission?
It can add a brief validation step, but the delay is generally minor compared to the time cost of reworking a denied claim later. If it’s configured as a hard stop, claims with flagged pairs will pause for review rather than transmitting immediately, which is the intended behavior, not a malfunction.
How often does the NCCI edit table need to be updated?
CMS publishes updated PTP edit tables quarterly. Whether your platform updates automatically or requires a manual refresh depends on the system, so this is worth confirming directly rather than assuming it’s handled.
What if my clearinghouse and PM system both have scrubbing rules?
It’s common for both layers to run some form of edit checking, which isn’t necessarily redundant since they may catch different things. Confirm with both your PM platform and your clearinghouse separately to understand exactly which edits each one is checking, so you’re not assuming coverage that one layer doesn’t actually provide.
Can I customize which code pairs get flagged?
Some platforms allow rule-level customization, such as setting specific pairs to hard-stop while others remain soft-flagged; others apply the same behavior across the entire NCCI table. Check your platform’s documentation or support team to find out what level of customization is available on your account.
Conclusion
NCCI edit checking is one of the highest-leverage settings in your billing workflow because it stops the most common CO 97 root cause before the claim ever leaves your system. The general pattern is the same everywhere: find the scrubbing rule settings, confirm NCCI/CCI edits are active, decide how strict the response should be, and verify the edit table is current. The exact screens will differ by platform and account setup, so confirm the specific steps with your platform’s current documentation or support team rather than relying on screenshots from an older version.
Manikandan is a Revenue Cycle Management (RCM) specialist with over 10 years of hands-on experience in US healthcare billing. He has worked extensively with commercial payers, Medicare, and Medicaid across multiple specialties including surgery, orthopedics, and radiology. Manikandan founded Medical Billing 101 to provide free, accurate denial code guides, CPT coding references, and Medicare billing resources for US medical billing professionals.