Pulmonology practices face billing challenges that most other specialties never encounter. Between pulmonary function test (PFT) coding rules, bronchoscopy modifier requirements, and overlapping critical care billing, even experienced billing teams struggle to capture every dollar earned.
Contact AMS Solutions for a free billing consultation and find out how much revenue your pulmonology practice could recover.
This guide breaks down the specific CPT codes, billing workflows, and denial-prevention strategies that pulmonology practices need to protect their revenue. Whether you run a small single-physician pulmonary clinic or a multi-provider group, the coding details covered here will help your team submit cleaner claims and collect more from every patient encounter.
Why Pulmonology Billing Is More Complex Than Most Specialties
Pulmonology sits at the intersection of diagnostic testing, procedural work, and chronic disease management. A single patient visit might involve spirometry, a bronchoscopy, and an evaluation and management (E/M) service, each with its own coding and documentation requirements.
Three factors make pulmonology billing especially difficult:
- Bundling rules for PFTs: The National Correct Coding Initiative (NCCI) bundles many pulmonary function test codes together. Billing CPT 94010 (basic spirometry) alongside CPT 94060 (bronchodilator response spirometry) on the same claim triggers automatic denials because 94060 already includes the pre-bronchodilator measurement.
- Multiple procedure discounts on bronchoscopy: When a bronchoscopy involves biopsy, lavage, and brushing in the same session, payers apply payment reductions to the secondary and tertiary procedures. Incorrect modifier use leads to underpayment or outright denials.
- Critical care overlap: Pulmonologists frequently provide critical care services (CPT 99291 and 99292) alongside procedures. Separating the time spent on critical care from procedural work requires careful documentation to avoid double-billing flags.
Essential PFT Billing Codes Every Pulmonology Practice Needs to Know
Pulmonary function testing carries its own family of CPT codes, and the ones that matter most day to day in a pulmonology practice are 94010, 94060, 94070, 94726, 94727 and 94729. Selecting the right code depends on the specific test performed, whether a bronchodilator was administered, and which components (professional vs. technical) your practice bills.
Core Spirometry Codes
| CPT Code | Description | Key Billing Notes |
|---|---|---|
| 94010 | Basic spirometry (FVC, FEV1, MVV) | Requires at least 3 acceptable flow-volume loops for 2026 standards |
| 94060 | Spirometry with bronchodilator response | Includes pre- and post-bronchodilator; do NOT bill 94010 separately |
| 94070 | Bronchial provocation testing (multi-stage) | Requires serial measurements; document each stage with times |
The most common PFT billing mistake is submitting both 94010 and 94060 on the same claim. CPT 94060 already includes the basic spirometry component. Billing both triggers NCCI edits and guarantees a denial for 94010.
Lung Volume and Diffusion Codes
| CPT Code | Description | Key Billing Notes |
|---|---|---|
| 94726 | Lung volumes by plethysmography | Standalone code, not an add-on; do not report with 94727 on the same date |
| 94727 | Gas dilution or washout for lung volumes | Cannot be billed with 94726 on the same date |
| 94729 | Diffusing capacity (DLCO) | The only add-on code in this group; report in conjunction with a primary pulmonary function test such as 94010, 94060, 94726 or 94727 |
DLCO testing (CPT 94729) is the only add-on code in this group, meaning it cannot be billed without a primary pulmonary function test code. Practices that accidentally submit 94729 as a standalone test face automatic rejection. Codes 94726, 94727 and 94728, by contrast, are standalone codes and should never be treated as add-ons. CMS publishes the bundling logic that governs these pairings in the National Correct Coding Initiative (NCCI) edits, which is the authoritative place to confirm a pairing before you bill it.
Professional vs. Technical Components
If your practice owns the spirometry equipment and employs the technician who performs the test, you bill the global service. If a hospital or independent lab owns the equipment, you bill only the professional component using modifier -26. Getting this wrong leads to duplicate billing flags when the facility also submits the technical component.
For a deeper understanding of how the full billing cycle works, from charge entry to final payment, see our guide on the seven stages of the healthcare revenue cycle.
Bronchoscopy Coding: Getting Paid for Every Procedure
Bronchoscopy is a significant revenue driver for pulmonology practices, but its coding complexity leads to frequent underpayment. The base code, CPT 31622, covers a diagnostic bronchoscopy with specimen collection by trapping or aspiration. Most bronchoscopy sessions involve additional procedures that require separate codes.
Common Bronchoscopy CPT Codes
| CPT Code | Procedure | Billing Considerations |
|---|---|---|
| 31622 | Diagnostic bronchoscopy with specimen collection | Base code; bundled into biopsy codes per NCCI |
| 31623 | Bronchoscopy with brushing or protected brushing | Report instead of 31622 when brushing is performed |
| 31624 | Bronchoalveolar lavage (BAL) | Use modifier -59 when performed in a different lobe than biopsy |
| 31625 | Endobronchial biopsy | Includes diagnostic component; do NOT also bill 31622 |
| 31628 | Transbronchial lung biopsy, single lobe | Covers one lobe only; report each additional lobe with add-on code +31632 |
| 31629 | Transbronchial needle aspiration biopsy (TBNA), initial lobe | Requires documentation of the specific sampling site; report each additional lobe with add-on code +31633 |
Talk to our billing specialists about bronchoscopy coding. AMS Solutions has managed pulmonology claims since 1992.
Modifier -59: The Key to Bronchoscopy Reimbursement
Modifier -59 (Distinct Procedural Service) is the most important tool in bronchoscopy billing. When a pulmonologist performs a transbronchial lung biopsy (31628) in the right upper lobe and a bronchoalveolar lavage (31624) in the left lower lobe, these are distinct services performed in separate anatomical sites. Without modifier -59 on the secondary procedure, the payer’s automated system will bundle the codes and pay only for the biopsy.
One distinction is worth drawing clearly, because getting it wrong costs real money. Modifier -59 separates two different procedures performed at distinct anatomical sites. Additional lobes sampled with the same technique are not a modifier -59 situation at all: they are reported with add-on codes, +31632 for each additional lobe of transbronchial lung biopsy and +31633 for each additional lobe of transbronchial needle aspiration. Appending modifier -59 instead of billing the add-on code is a common source of under-payment.
To support the modifier, the operative report must clearly document:
- The specific lobe or segment where each procedure was performed
- The clinical indication for each separate procedure
- The sequence and timing of each intervention
Vague documentation like “bronchoscopy with biopsy and lavage” almost always results in denied claims when modifier -59 is appended.
Critical Care Billing for Pulmonologists
Many pulmonologists split their time between the outpatient clinic and the ICU. Critical care billing (CPT 99291 for the first 30-74 minutes, CPT 99292 for each additional 30-minute block) comes with strict rules about what time counts.
Time spent performing separately billable procedures must be subtracted from critical care time. If a pulmonologist spends 90 minutes at a critically ill patient’s bedside but 25 of those minutes are spent performing and interpreting a bedside bronchoscopy, only 65 minutes count toward critical care codes.
Documentation Requirements for Critical Care
Payers audit critical care claims from pulmonologists more frequently than from other specialties because of the procedure overlap. Your documentation should include:
- Total bedside time: Recorded to the minute, not in general terms like “over 30 minutes”
- Procedure time deducted: Specific minutes spent on each separately billed procedure
- Medical decision-making: The conditions assessed and treatment decisions made during the critical care period
- Critically ill criteria: Why the patient met the threshold for critical care (organ failure, hemodynamic instability, respiratory failure)
Missing any of these elements gives auditors grounds to downcode or deny the claim entirely.
Oxygen Therapy and Pulmonary Rehabilitation Billing
Two additional revenue areas that pulmonology practices often underbill are home oxygen therapy and pulmonary rehabilitation.
Home Oxygen Therapy
Qualifying patients for home oxygen requires arterial blood gas (ABG) or pulse oximetry documentation showing SpO2 at or below 88% at rest, during exercise, or during sleep. CMS discontinued Certificates of Medical Necessity, including the CMS-484 for oxygen, along with DME Information Forms, effective January 1, 2023; claims submitted with those forms are now rejected (CMS MLN Matters SE22002). Home oxygen is now supported by a standard written order from the treating practitioner together with medical record documentation of the qualifying test results, the diagnosis, and the patient’s continuing need for oxygen. When the chart does not clearly carry the qualifying testing, the claim is what fails.
Pulmonary Rehabilitation
Pulmonary rehabilitation is reported per session with CPT 94625 (without continuous oximetry monitoring) or CPT 94626 (with continuous oximetry monitoring). The distinction between them is monitoring, not sequence, so 94626 is not a “subsequent session” code. CMS sets out both descriptors and the program requirements in Billing and Coding article A52770. Pulmonary rehabilitation is covered by Medicare for patients with moderate to severe COPD, and by many commercial payers for other chronic respiratory conditions. Each session must be documented with:
- Individualized treatment plan updates
- Exercise metrics (duration, intensity, patient response)
- Educational components delivered
- Progress toward measurable goals
Many practices leave pulmonary rehabilitation revenue on the table simply because they do not document each session with enough detail to support medical necessity.
How to Reduce Claim Denials in Your Pulmonology Practice
Denial management starts before the claim is submitted. The most effective pulmonology practices build denial prevention into their daily workflow rather than reacting after the fact.
5 Steps to Lower Denial Rates
- Verify insurance eligibility before every visit. Pulmonary function tests and bronchoscopies often require prior authorization. Skipping eligibility checks is the fastest path to preventable denials.
- Link every procedure to a specific ICD-10 code. Payers reject claims when the diagnosis does not support the test ordered. For example, PFTs billed under R06.00 (dyspnea, unspecified) are more likely to be denied than those linked to J44.1 (COPD with acute exacerbation) because unspecified codes fail to demonstrate medical necessity.
- Audit PFT claims for bundling errors weekly. Set up a recurring review of all PFT claims to catch 94010/94060 bundling mistakes, standalone add-on codes, and missing modifiers before submission.
- Standardize bronchoscopy operative note templates. Build templates that require the surgeon to document the specific lobe, procedure type, and clinical indication for each intervention. This prevents vague notes that undermine modifier -59 claims.
- Track denials by CPT code, not just by volume. Knowing that “10% of claims were denied” is less useful than knowing “45% of 31624 claims were denied due to missing modifier -59.” Code-specific tracking reveals the root cause.
For more on how Medicare and Medicaid rules affect your billing workflow, read our article on navigating Medicare and Medicaid billing guidelines.
When Should a Pulmonology Practice Outsource Billing?
Not every practice needs to outsource, but several warning signs suggest your in-house billing is costing you money:
- Your denial rate exceeds 8% (a commonly cited target for well-managed practices is the mid-single digits)
- Claims older than 90 days make up more than 15% of your accounts receivable
- You have lost billing staff and cannot find qualified replacements who understand pulmonology coding
- Your collections have declined even as patient volume has stayed steady or grown
- You spend more time managing billing than treating patients
A specialized billing partner understands the NCCI edits, modifier rules, and documentation requirements specific to pulmonology. AMS Solutions has served medical practices across more than 28 medical specialties since 1992, with dedicated billing professionals who understand the nuances of respiratory medicine coding.
Get a free billing assessment from AMS Solutions. Our team will review your current collections and identify where you are leaving money on the table.
Credentialing Considerations for Pulmonology Practices
Before you can bill for pulmonology services, every provider in your practice must be credentialed with each insurance carrier. Gaps in credentialing mean claims are denied at the front door, regardless of how well they are coded.
Common credentialing issues for pulmonology practices include:
- New providers joining the practice without completed enrollment, creating a 60 to 90 day revenue gap
- Expired Medicare or Medicaid enrollment that blocks all government-payer claims
- Missing subspecialty designations (pulmonary medicine, critical care medicine, or sleep medicine) that trigger claim rejections
AMS Solutions handles provider credentialing for Medicare, Medicaid, BCBS, and commercial carriers, so your team can focus on patient care instead of paperwork.
Frequently Asked Questions
What CPT codes are used for pulmonary function tests?
The primary PFT CPT codes are 94010 (basic spirometry), 94060 (spirometry with bronchodilator response), 94070 (bronchial provocation testing), 94726 (lung volumes by plethysmography), 94727 (lung volumes by gas dilution or washout) and 94729 (diffusing capacity/DLCO). Of these, only 94729 is an add-on code that must be reported alongside a primary pulmonary function test. Codes 94726, 94727 and 94728 are standalone codes.
Can I bill CPT 94010 and 94060 together?
No. CPT 94060 includes the pre-bronchodilator spirometry that 94010 covers. Billing both on the same claim violates NCCI bundling rules and will result in a denial for 94010. Always bill 94060 alone when bronchodilator response testing is performed.
How do I bill for a bronchoscopy with multiple procedures?
Report the primary procedure code (such as 31625 for endobronchial biopsy) and add secondary procedure codes with modifier -59 when they are performed in a different anatomical site. The operative note must document the specific lobe and clinical indication for each separate procedure to support the modifier.
What is the most common reason for pulmonology claim denials?
NCCI bundling errors are the leading cause. This includes billing 94010 with 94060, billing 31622 alongside a biopsy code that already includes the diagnostic component, and submitting add-on codes like 94729 without a primary procedure code.
Does Medicare cover pulmonary rehabilitation?
Yes. Medicare covers pulmonary rehabilitation for patients with moderate to severe COPD. Each session is reported with CPT 94625 (without continuous oximetry monitoring) or CPT 94626 (with continuous oximetry monitoring); the choice depends on whether continuous oximetry was monitored during that session, not on whether it was the first session or a later one. Coverage typically allows up to 36 sessions, with an additional 36 sessions available if medical necessity is documented. Each session must include individualized exercise training and documented progress.
How can outsourcing billing help a pulmonology practice?
A specialized billing company handles PFT coding rules, bronchoscopy modifier requirements, credentialing, and denial management. Practices that outsource to a billing partner like AMS Solutions typically see lower denial rates and faster collections because the billing team works with pulmonology-specific codes daily.
