How to Use Modifier 59: Documentation and Billing Best Practices

Why Modifier 59 Matters in Medical Billing

Modifier 59 is one of the most commonly used—and misused—CPT modifiers in outpatient billing. It plays a central role in helping providers differentiate services that would otherwise be bundled by Medicare or commercial payers. When used correctly, it can support payment for clinically distinct procedures performed on the same day. When used incorrectly, however, it can trigger claim denials or audits.

This article explains what modifier 59 is, how it should be applied, and why it matters for compliance and revenue cycle performance. We’ll also look at an example and clarify the difference between modifier 59 and the related subset of X modifiers (XE, XS, XP, XU).

What Is Modifier 59?

Modifier 59 is defined by the Centers for Medicare & Medicaid Services (CMS) as a means to identify “distinct procedural services.” It’s used to indicate that procedures typically considered bundled—meaning not separately reimbursed—are in fact independent and should be billed separately due to different sessions, anatomical sites, or procedures¹.

Modifier 59 should be used only when there is no better, more descriptive modifier available. CMS has explicitly stated that providers should use the X{EPSU} modifiers instead of modifier 59 when possible¹.

Common justifications for modifier 59 include:

• A separate patient encounter

• A different anatomical site

• A separate incision or injury

• A different session

Importantly, modifier 59 should not be used solely to bypass National Correct Coding Initiative (NCCI) edits. Its use must be clinically supported and documented.

How to Apply Modifier 59 Correctly

Modifier 59 is appended to one of the two CPT codes involved in an NCCI edit pair. Typically, it’s added to the lesser-valued procedure to justify separate payment.

Here’s an overview of when to consider using modifier 59:

1. Distinct Encounter or Session

If two procedures are performed at separate times on the same day—such as one in the morning and one in the afternoon—modifier 59 can be appropriate.

2. Different Anatomical Sites

When procedures target entirely different body parts (e.g., left vs. right side), modifier 59 may apply if no more specific modifier exists (e.g., RT/LT or 50).

3. Separate Lesions or Injuries

In wound care or dermatological services, if multiple lesions are treated with similar procedures, modifier 59 helps distinguish each service if they’re performed on unrelated areas.

4. Documentation

The clinician’s documentation must clearly support the use of modifier 59. Lack of detailed clinical notes is a common reason payers reject claims with this modifier.

Common Example of Modifier 59 in Use

Example Scenario:

A physical therapist provides therapeutic exercise (CPT 97110) and manual therapy (CPT 97140) during the same visit.

According to NCCI edits, 97110 and 97140 are considered a linked pair. In general, 97140 would be considered inclusive of 97110 and not separately reimbursed—unless the services are performed in separate body regions or at separate times and are clinically distinct.

Correct Use:
The therapist applies manual therapy to the cervical spine and provides therapeutic exercises for lower-extremity post-op rehabilitation. Modifier 59 is appended to CPT 97140 to indicate these are distinct services:

• 97110 – Therapeutic exercises (no modifier)

• 97140–59 – Manual therapy (modifier 59 appended)

Documentation must show:

• Distinct body regions treated

• Clinical rationale for each service

• Clear start and stop times for time-based codes

X Modifiers: A Better Alternative?

In 2015, CMS introduced four subset modifiers—XE, XP, XS, XU—to replace modifier 59 when more specific context is available¹. These are:

• XE – Separate encounter

• XP – Separate practitioner

• XS – Separate structure or site

• XU – Unusual non-overlapping service

While modifier 59 is still accepted, CMS prefers the use of these X modifiers to improve claims accuracy and reduce audit risk. Commercial payers may or may not recognize them, so provider organizations should check with each payer before making the switch.

Modifier 59 vs. Modifier 51: Key Differences

Modifier 59 and modifier 51 are often confused, but they serve different purposes and should not be used interchangeably.

• Modifier 59 is used to indicate that two procedures, typically bundled under Medicare’s NCCI edits, are distinct and should be reimbursed separately.

• Modifier 51 identifies multiple procedures performed during the same session by the same provider. It does not imply distinctness or unbundling—it simply flags that multiple services were performed.

When to use modifier 51:

• When multiple surgical or diagnostic procedures are performed during the same encounter

• The procedures are not part of an NCCI edit pair

• No modifier 59 or X modifier is needed to justify distinct services

Key Difference:
Modifier 59 justifies separate reimbursement by indicating a distinct procedural service. Modifier 51 does not indicate clinical distinction; it’s primarily used for sequencing and payment reduction purposes when multiple services are reported.

Example: If a patient receives manual therapy (97140) and therapeutic exercise (97110) to different anatomical areas, and they are considered an NCCI edit pair, modifier 59 may be appropriate—not modifier 51.

Modifier 59 vs. Modifier 25: Distinct Procedures vs. Separate E/M Services

Modifier 25 is another commonly misunderstood modifier that differs significantly from modifier 59.

• Modifier 59 applies to procedural CPT codes (e.g., therapy services, minor surgeries) to identify that services are separate and independent.

• Modifier 25 applies only to Evaluation and Management (E/M) services and is used to indicate that an E/M service was significant and separately identifiable from another procedure performed on the same day by the same provider.

When to use modifier 25:

• An E/M service (e.g., 99213) is provided in addition to a procedure (e.g., wound debridement or joint injection)

• The E/M service addresses a different issue or goes beyond the pre-service work typically included in the procedure

Key Difference:
Modifier 59 distinguishes between procedural services, while modifier 25 distinguishes an E/M service from a procedure on the same day.

Example: A patient receives a full musculoskeletal evaluation (99203) and a same-day therapeutic intervention (97110). If the evaluation is separately identifiable and not part of the pre-service work of the therapy, modifier 25 would be appended to 99203—not modifier 59.

Billing Compliance Considerations

Modifier 59 misuse is one of the most cited issues in billing audits. The U.S. Department of Health & Human Services Office of Inspector General (OIG) has published multiple reports flagging improper use of modifier 59 as a compliance risk.

To reduce errors:

• Educate clinicians and coders on when and how to apply modifier 59 or X modifiers

• Audit claims regularly to verify documentation supports modifier use

• Use claim scrubber tools that flag inappropriate modifier pairings or usage patterns

• Refer to payer-specific guidelines, as Medicare, Medicaid, and commercial plans may differ

Using Modifier 59 with Accuracy and Confidence

Modifier 59 can support accurate reimbursement when used appropriately. It helps differentiate separate services that would otherwise be denied or bundled. But improper use—especially when documentation doesn’t support it—can raise red flags, delay payments, or result in clawbacks.

Disclaimer: The information contained in this document does not, and is not intended to, constitute legal, billing, or regulatory advice or guidance. All information, content, and material is for general information purposes and independent review and/or counsel should be obtained before making any legal or billing decisions.

References

1. CMS. Proper Use of Modifiers 59 and X{EPSU}. https://www.cms.gov/files/document/proper-use-modifiers-59-xe-xp-xs-xu.pdf