How does MIPS quality reporting work for athenahealth practices?

Under the Merit-based Incentive Payment System (MIPS), clinicians report at least 6 quality measures for the full calendar year, and the Centers for Medicare & Medicaid Services (CMS) scores them against national benchmarks. For the 2026 performance year, quality is 30% of a 0 to 100 final score, and that score sets a Medicare payment adjustment two years later, in 2028. athenaOne tracks your measures, shows daily preview scores, and can submit the data for you, but the score is decided by what your team documents all year, not by what happens at submission time.

What are the MIPS performance categories and weights?

MIPS combines four performance categories into one final score. For the 2026 performance year, CMS weights them as follows when no category is reweighted, according to the CMS 2026 Quality Quick Start Guide:

Small practices (15 or fewer clinicians) have Promoting Interoperability reweighted to 0% automatically unless they submit it, and CMS shifts that weight to other categories, as the CMS 2026 Small Practices Quick Start Guide explains. The performance threshold is 75 points: a score above 75 earns a positive adjustment, 75 is neutral, and below 75 is negative, down to a maximum of -9%, according to the CMS 2027 final rule fact sheet.

How do quality measures work?

Quality is the category your staff touches every day, because each measure is a numerator and a denominator built from visits, diagnoses, results and documentation. The CMS 2026 Quality Quick Start Guide sets these rules for 2026:

1. Six measures. Traditional MIPS reporters select at least 6 quality measures from 190 available, including 1 outcome or high-priority measure. MIPS Value Pathway (MVP) reporters select 4 from their pathway.
2. Full year. The performance period runs January 1 to December 31, 2026.
3. Data completeness. You must report on at least 75% of patients who meet each measure's denominator. CMS has kept 75% through the 2028 performance year.
4. Case minimum. Each measure needs at least 20 cases to be scored against a benchmark. Measures that miss it earn 0 points, or 3 points for small practices.

Collection type is how the data is gathered, and each has its own measure specification:

MIPS Value Pathways (MVPs) are smaller, specialty or condition-based sets of measures and activities. CMS listed 27 MVPs for 2026 and requires registration in advance, per the Small Practices Quick Start Guide.

What changes in the 2027 performance year?

CMS released the 2027 final rule on November 4, 2026. The 2027 Quality Payment Program final rule fact sheet makes these changes for the 2027 performance year (2029 payment year):

• Core measures replace the outcome or high-priority requirement. Traditional MIPS reporters must include one MIPS core measure among their 6, and MVP reporters one among their 4. CMS designated 78 measures as core. Small practices are exempt. Others who skip it without attesting that none applies get 0 of 10 points for one required measure.
• Three new MVPs: diabetic disease, hospitalist and hypertension.
• Traditional MIPS ends after the 2030 performance period. From 2031, clinicians outside an Alternative Payment Model must report an MVP. The CMS press release notes this is two years later than proposed.
• Threshold unchanged. The performance threshold stays at 75 points through the 2028 performance period.

For a primary care practice, the practical step is to check, before January, whether one of your current six measures carries the core designation, and whether an MVP fits your specialty now that the end date for traditional MIPS is fixed.

Why does the two-year payment lag matter?

The adjustment you feel in a given year reflects work from two years earlier. For 2026, the CMS Small Practices Quick Start Guide lays out the sequence: CMS expects final scores in mid-June 2027, and the adjustment applies claim by claim to covered professional services billed in 2028. The 2027 fact sheet gives the 2026 submission window as January 4 to March 31, 2027.

Two consequences follow. First, a missed screening in March 2026 is a payment question in 2028, long after anyone remembers why it was missed. Second, by the time the score arrives, the next year is already half over, so the score itself is a poor steering tool. You need your own view during the year.

How does athenahealth support MIPS reporting?

athenaOne includes several tools for MIPS, described in athenahealth's own help pages:

• MIPS Dashboard. Under Quality, the MIPS Dashboard shows eligibility, a Clinician Report Card, measure-level numerators and denominators, and CMS preview scores for Quality, Promoting Interoperability and Improvement Activities. athenahealth says preview scores update daily. Cost does not appear.
• Patient-level detail. The dashboard does not list patients. athenahealth points users to the Quality Management Report for patient-level data.
• Enrollment tracks. In the Quality Program Enrollment setup, the default For Attestation track means athenahealth submits for you, and enrolled measures appear on the dashboard, the Quality Management Report, the eCQM Data Report and the Quality tab in the patient chart. The Not-for-Attestation track is for practices that self-submit or only monitor.
• Submission. athenahealth describes itself as a CMS-approved qualified registry that submits when requirements, including clinician sign-off, are met.
• No claims-based reporting. athenahealth states on its MIPS Reporting Activity Report page that it no longer supports claims-based MIPS reporting, so small practices planning on Part B claims should confirm their route early.

How should a practice monitor measures during the year?

The tools are there. What most practices lack is a routine. We suggest a monthly quality review with an owner, a fixed agenda and a short list of actions:

1. Confirm enrollment in January. Check that every eligible clinician and measure is enrolled in the right track and that new clinicians are handled before their first visits.
2. Watch data completeness and case counts first. A measure under 75% completeness or 20 cases scores poorly however good the care is. Catch it in spring, not December.
3. Read performance by clinician. The Measure Performance view and Clinician Report Card show who is behind. Share results with clinicians monthly, not once a year.
4. Work patient lists, not percentages. Pull patient-level gaps from the Quality Management Report into pre-visit planning and outreach, the same workflow we describe in our HEDIS gap closure article.
5. Check documentation habits. Many misses are care that happened but was recorded in free text or a scanned document instead of the structured field the measure reads.
6. Put quality next to operations. A few MIPS measures belong on the same monthly practice KPI scorecard as access and revenue, so leaders see them together.

Practices that want trend lines across years, sites or payers often move this reporting into a warehouse built on athenaOne Data View, covered in our Data View article and our analytics and BI architecture service.

How we approach this

Ben Miller built a v1 ambulatory quality measure engine and its Tableau reporting layer, then scaled it with engineering, operations and clinical teams to HEDIS, MIPS and clinician-level reporting for 2M+ primary care patients across about 2,600 sites of care in 19 states. We bring that pattern to independent practices: write each measure definition down, check it against what athenaOne reports, and give each team a list it can act on. Where the gap is process rather than data, our strategic operations work sets up the review routine and owners.

Where to start

This week, open the MIPS Dashboard, export the Measure Performance view, and mark every measure under 75% data completeness or under 20 cases. Then check your six measures against the 2027 core measure list once CMS posts the 2027 specifications. If you want a second set of eyes on the plan, book a free strategic assessment.