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CMS Sheds New Light on Proper Use of Modifier 59

by | Sep 28, 2022

Due to the common misuse of this modifier, the Centers for Medicare & Medicaid Services recently issued important new guidance on its proper use.

Current Procedural Terminology (CPT) codes can’t account for every exact circumstance and situation. That’s why the American Medical Association (AMA) created modifiers that can be used to report or indicate that a service or a procedure that hasn’t changed in its definition or coding assignment has nevertheless been altered by some specific circumstance. Among the most commonly used—and misused—of these modifiers is modifier 59, which indicates that two or more procedures were performed at the same visit but to different sites on the body, different patient samples, or different encounters. In March 2022, the Centers for Medicare & Medicaid Services (CMS) issued important new guidance on proper use of the modifier.

Modifier 59

The CPT Manual defines modifier 59 as a “Distinct Procedural Service.” According to the manual:

“Under certain circumstances, it may be necessary to indicate that a procedure or service was distinct or independent from other non-E/M (Evaluation/Management) services performed on the same day. Modifier 59 is used to identify procedures/services, other than E/M services, that are not normally reported together, but are appropriate under the circumstances. Documentation must support a different session, different procedure or surgery, different site or organ system, separate incision/excision, separate lesion, or separate injury (or area of injury in extensive injuries) not ordinarily encountered or performed on the same day by the same individual.”     

However, modifier 59 is a kind of last resort. “When another already established modifier is appropriate, it should be used rather than modifier 59,” according to the manual. Modifier 59 should be used only “if no more descriptive modifier is available, and the use of modifier 59 best explains the circumstances.”

Another common pitfall is using the 59 modifier to prevent a service from being bundled or added in with another service on the same claim. Chapter 1 of the National Correct Coding Initiative (NCCI) Policy Manual explains that modifiers may be appended to Healthcare Common Procedure Coding System (HCPCS)/CPT codes only if the clinical circumstances justify the modifier’s use. What you can’t do is use a modifier solely to bypass a NCCI procedure to procedure (PTP) edit if the clinical circumstances do not justify its use. If the Medicare program imposes restrictions on the use of a modifier, the modifier may only be used to bypass an NCCI PTP edit if the Medicare restrictions are fulfilled.

The New CMS Guidance

In March 2022, CMS published MLN1783722 providing updated information on the use of modifier 59 under the Medicare NCCI. Providers need to be aware of the guidance on the limitations and appropriate reporting of this modifier to the extent that PTP edits for CPT codes are linked to a Correct Coding Modifier Indicator. Key points in MLN1783722:

  • Indicator “0”: Never report the indicated codes together by the same provider for the same beneficiary on the same date of service. If you do report the codes together on the same date of service, the Column One code is eligible for payment and Medicare will deny the Column Two code.
  • Indicator “1”: The code pair may be reported together only in defined circumstances by using specific NCCI PTP-associated modifiers.

CMS Warns Against Misuse of Modifier 59

In addition, CMS says that modifier 59 is associated with considerable abuse and high levels of manual audit activity leading to reviews, appeals, and even civil fraud and abuse cases. The primary issue associated with the 59 modifier is that it’s defined for use in a wide variety of circumstances, such as to identify:

  • Different encounters;
  • Different anatomic sites; and
  • Distinct services.

Accordingly, CMS states that the -59 modifier is:

  • Infrequently (and usually correctly) used to identify a separate encounter;
  • Less commonly (and less correctly) used to define a separate anatomic site; and
  • More commonly (and frequently incorrectly) used to define a distinct service.

The -59 modifier often overrides the edit in the exact circumstance for which CMS created it in the first place. CMS believes that more precise coding options coupled with increased education and selective editing is needed to reduce the errors associated with this overpayment.

Modifier 59 should also not be appended to an E/M service to report a separate and distinct E/M service with a non-E/M service performed on the same date (see modifier 25).                                            

The 4 Modifier 59 Subsets

CMS has established four modifier subsets that may be used in lieu of modifier 59 to provide greater reporting specificity in situations where modifier 59 was previously reported. They may be used in lieu of modifier 59 whenever possible. The modifiers are defined as follows:

  • XE - Separate Encounter - A service that is distinct because it occurred during a separate encounter. (This modifier may only be used to describe separate encounters on the same date of service);
  • XS - Separate Structure - A service that is distinct because it was performed on a separate organ/structure;
  • XP - Separate Practitioner - A service that is distinct because it was performed by a different practitioner;
  • XU - Unusual Non-Overlapping Service - The use of a service that is distinct because it does not overlap usual components of the main service.

While CMS will continue to recognize the -59 modifier in many instances, the agency or Medicare Administrative Contractors (MACs) may selectively require a more specific “-X” modifier for billing certain codes at high risk for incorrect billing. For example, a particular NCCI code pair may be identified as payable only with the -XE separate encounter modifier, but not the -59 or other -X modifiers. Since the -X modifiers are more selective versions of the 59 modifier, you shouldn’t include both modifiers on the same line.

MAC and Commercial Contractor Modifier 59 Policies

It should also be noted that many MACs and commercial payers have established their own -59 modifier policies. Additionally, the MolDX program has published an updated article for Billing and Coding: MolDX: Testing of Multiple Genes.

Helpful Hint

If you need help with policy formation and compliance program effectiveness, the 37-page Chapter 1 in the NCCI Manual is loaded with detailed information that can assist you.

The American Academy of Professional Coders (AAPC) advises: When appending modifier 59 to break a CCI (Correct Coding Initiative) edit, you should always append the modifier to the secondary (“column 2”) code. Example: The column one/column two code edit with column 1 CPT code 38221 (diagnostic bone marrow biopsy) and column 2 CPT code 38220 (diagnostic bone marrow aspiration) includes two distinct procedures when performed at separate anatomic sites or separate patient encounters. In such circumstances, it would be appropriate to report the -59 modifier with CPT 38220.

If both procedures are performed at the same site at the same patient encounter, modifier 59 should not be reported because it bundles with the biopsy code. Instead, report CPT 38222 (bone marrow aspiration and biopsy). Example: Apolipoprotein A1 and B are determined on the same date of service and patient sample. The same CPT code (82172, Apolipoprotein, each) is used to report both assays. The second unit of service should be reported using the 59 modifier to prevent denial as a duplicate service.

The -59 modifier is applicable to all claims to all payers. It is part of the national coding requirements under the Administrative Simplification section of the Health Insurance Portability and Accountability Act of 1996 (HIPAA), so it’s essential that labs become familiar with how to use this modifier correctly.


Diana W. Voorhees, M.A., CLS, MT, SH, CLCP, CPCO, is principal in DV & Associates, Inc., Salt Lake City, UT, which makes no representation, guarantee or warranty, expressed or implied, that the information provided is free of error, and will bear no responsibility or liability for results or consequences of its use.

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