The Physician Quality Reporting System (PQRS): What is it and Where Did it Go?

The Physician Quality Reporting System (PQRS) is one phase of an evolving history of long-term U.S. programs created to assess and facilitate high-quality care across the healthcare system. Developed by the Centers for Medicare and Medicaid Services (CMS), PQRS is a “legacy” public reporting program, established in 2006 and ending in 2016, designed to collect data submitted by Eligible Professionals (EPs) on quality measures for covered services delivered to Medicare Part B fee-for-service (FFS) beneficiaries. Originally constructed to incentivize physicians to voluntarily participate in reporting quality data to CMS, PQRS transitioned into a penalty program in 2011 before its official “end” and integration into the Quality Payment Program (QPP) in 2017.

Brief History Leading up to PQRS

In 1965, President Lyndon B. Johnson signed into law an amendment to the Social Security Act of 1935 that would lead to the formation of Medicare, Medicaid, and the Centers for Medicare and Medicaid Services (CMS). Since that time, oversight into the quality of health care in the United States has been ongoing, specifically regarding patients in the Medicare system. Throughout the 60’s and 70’s Congress experimented with utilization committees and professional review organizations without much success, until 1983 with the implementation of Peer Review Organizations (PROs). PROs were created to monitor, control, and improve the cost and quality of care received by Medicare beneficiaries, and they were given the authority to design process-focused and outcome-focused solutions based on their quality data findings.

In 1992, as the focus on data-driven quality improvements continued, the Health Care Quality Improvement Initiative (HCQII) aimed to “create a patient care algorithm system based on clinical guidelines and information provided by claims history and data set. This was implemented in an effort to achieve evidenced-based continuous quality improvement” (Marjoua). Over the next decade, additional models were initiated to focus on quality improvement, including the National Surgery Quality Improvement Project (NSQIP) in 1994, and the Surgical Care Improvement Program (SCIP) in 2003, which moved from a voluntary to a mandatory publicly reported system, with “participation incentivized by a Medicare payment that would otherwise be withheld for non-participation” (Marjoua). Public reporting requirements continued to expand with the introduction of the Hospital Inpatient Quality Reporting Program (IQR) in 2003, as well as the Tax Relief and Health Care Act of 2006 (TRHCA), which established the Physician Quality Reporting Initiative (PQRI). PQRI was a “pay-for-reporting” initiative that was refined and enhanced by the Medicare, Medicaid, and SCHIP Extension Act in 2007, the Patients and Providers Act of 2008, and finally the Affordable Health Care Act of 2010. One year later, PQRI would “graduate” from a temporary initiative into what we now know as the Physician Quality Reporting System (PQRS).

What is PQRS?

The Physician Quality Reporting System (PQRS) is a national program that links the reporting of quality data to physician payment. Initially a voluntary quality reporting program, with positive payment incentives, PQRS became a mandatory, penalty-only program in 2015, linking Medicare payments to the quality of care delivered to Medicare patients. Specifically, PQRS pertained to Medicare Physician Fee Schedule (MPFS) services furnished to Medicare Part B beneficiaries, including Railroad Retirement Board, Medicare Secondary Payer, and Critical Access Hospitals (CAH) Method II. The program applies a downward payment adjustment to EPs identified on claims by their individual National Provider Number (NPI) and Tax Identification Number (TIN), or group practices, who do not satisfactorily report data on quality measures.

In its 2016 implementation guide, CMS defines PQRS as “a quality reporting program that uses negative payment adjustments to promote reporting of quality information by individual EPs and group practices.” In other words, PQRS uses the risk of negative payment adjustments to motivate physicians, influence their behavior, and hold them accountable to provide high-quality, cost-efficient care, and to report on that care.

Below are the high-level steps in the PQRS process for program year 2016:

  • EPs and group practices submit quality measure data on professional services provided and paid for under the Medicare Physician Fee Schedule (MPFS) for January 1, 2016 through December 31, 2016.
  • CMS completes a quality review to analyze the data for possible 2018 negative payment adjustments.
  • CMS gives feedback reports for EPs and group practices for review.
  • EPs and group practices can request an informal review of the CMS quality review findings, and CMS will make a final decision on if proper conclusions were made.
  • EPs and group practices provide 2018 services to Medicare Part B beneficiaries with a possible negative payment adjustment, based on quality data reported in 2016.

Although reporting is mandatory, CMS encourages providers to participate in PQRS explaining that it gives them an opportunity to “assess the quality of care they are providing to their patients, helping to ensure that patients get the right care at the right time. By reporting PQRS quality measures, providers…can quantify how often they are meeting a particular quality metric, [and by] using the feedback report provided by CMS, EPs can compare their performance on a given measure with their peers.”

For 2016, reports show that the majority of EPs successfully reported under PQRS and avoided the downward payment adjustment. EPs and group practices that did not satisfactorily report 2016 data on quality measures incurred a -2% payment adjustment for Medicare services provided in 2018. Furthermore, EPs and group practices may also have been subject to an additional and separate payment adjustment from one or both of the following legacy programs: the Value-based Payment Modifier (Value Modifier) and the Electronic Health Record (EHR) Incentive Program.

The PQRS timeline

During the final PQRS year, CMS defined 2016 eligible professionals (EPs) as the following:

EPs and group practices were encouraged to determine the best measures, associated domains, and reporting mechanism(s) applicable for their specific situations.

In 2016, there were approximately 281 quality measures in the PQRS measures set. CMS underscores the significance of reporting on applicable quality measures by explaining that “they are tools that help us measure or quantify health care processes, outcomes, patient perceptions, and organizational structures and/or systems that contribute to overall health care.” PQRS required the reporting of 9 measures (1 cross cutting) across 3 of the six National Quality Strategy (NQS) domains:

  • Communication and Care Coordination
  • Community / Population Health
  • Effective Clinical Care
  • Efficiency and Cost Reduction
  • Patient Safety
  • Person and Caregiver-Centered Experience and Outcomes

(See the following link for a comprehensive spreadsheet of all 2016 measures, their numbers, description, NQS domain, type, developer/steward, reporting method, group, specifications, and whether it is a crosscutting measure and if it is used in other reporting programs:

EPs could choose to report as individuals or as a group practice, utilizing six possible reporting mechanisms:

  • Medicare Part B Claims
  • Electronically via Certified Electronic Health Record Technology (CEHRT)
  • Qualified PQRS Registry
  • Qualified Clinical Data Registry (QCDR)
  • Group Practicing Reporting Option (GPRO) via Web Interface
  • CMS Certified Survey Vendor—Consumer Assessment of Healthcare Providers and Systems (CAHPS)

Where Did PQRS Go?

In 2015, Congress passed the Medicare Access and CHIP Reauthorization Act (MACRA), a bill designed for Medicare payment reform, aimed at lowering healthcare costs and improving the quality of patient care. MACRA ended the Sustainable Growth Rate (SGR) formula and required the Centers for Medicare and Medicaid Services (CMS) to implement a new incentive program called the Quality Payment Program (QPP). The QPP has two payment tracks: the Merit-based Incentive Payment System (MIPS) and the Advanced Alternative Payment Model (AAPM).

The Merit-based Incentive Payment System (MIPS) combines the Physician Quality Reporting System (PQRS), the Value-based Payment Modifier (Value Modifier), and the Electronic Health Record (EHR) Incentive Program into one, performance-based payment system. As noted, 2016 was the last program and reporting year for PQRS, and data reported in 2016 would affect any negative payment adjustments applied in 2018, overlapping with the 2017 implementation of MIPS under the Quality Payment Program (QPP).  

Here’s how the three legacy programs transition into the newly defined MIPS performance categories, along with their 2019 percentages toward final scores:

(For more details and a CMS timeline on the transition from PQRS to MIPS, see the following link:

(For a deeper dive into the Quality Payment Program, see the “MACRA Made Easy” article here:

Since 2007, CMS has relied heavily on the Physician Quality Reporting System (PQRS) to increase physician accountability and to facilitate the improvement and delivery of high-quality care for Medicare beneficiaries. With its integration into the Merit-based Incentive Program (MIPS), PQRS has officially ended as a stand-alone program, but it has given MIPS a structure and momentum that may help CMS to achieve its goal of providing effective, safe, efficient, patient-centered, equitable, and timely health care for all Americans.


North Texas Clinically Integrated Network, Inc. (dba TXCIN) is a non-profit ACO that began in late 2014. A small group of health care, independent physicians aligned to initiate clinical integration and value-based contracting. Partnering with RevelationMD and its state-of-the art information platform, TXCIN has become one of the largest, independent networks of physicians in North Texas.


Anumula, N. and P.C. Sanelli. “Physician Quality Reporting System.” Health Care Reform Vignette. December 2011. Retrieved February 6th, 2019. “2015 Physician Quality Reporting System (PQRS): Implementation Guide.” October 2015. Retrieved February 6th, 2019. “2016 Physician Quality Reporting System (PQRS): Understanding 2018 Medicare Quality Program Payment Adjustments.” March 2016. Retrieved February 6th, 2019. “2018 Physician Quality Reporting System (PQRS): Payment Adjustment Resource Document.” September 2017. Retrieved February 6th, 2019.

Heilman, Erin. “The History of Quality Reporting.” March 24, 2017. Retrieved February 6th, 2019.

Jones, Carol and Molly MacHarris. “Transitioning from the Physician Quality Reporting System (PQRS) to the Merit-based Incentive Payment System (MIPS).” Medicare Learning Network. January 24, 2017. Retrieved February 6th, 2019.

Marjoua, Youssra and Kevin J. Bozic. “Brief History of Quality Movement in US Healthcare.” Current Reviews in Musculoskeletal Medicine. Vol. 5, 4. Published online September 9th, 2012. Retrieved February 6th, 2019.

Unknown. “Physician Quality Reporting System (PQRS).” Society of Nuclear Medicine & Molecular Imaging. Date unknown. Retrieved February 6th, 2019.


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