MIPS via EHR (CEHRT): Direct Submission Guide

EHR-based MIPS reporting means submitting MIPS data directly from a Certified EHR (CEHRT) to the Centers for Medicare & Medicaid Services (CMS). Three performance categories move through the EHR: Quality, Promoting Interoperability, and Improvement Activities. 

CMS calculates Cost from Medicare Part B claims instead. Submission happens in the QRDA III format, by file upload on qpp.cms.gov or through an API. The submitting EHR must be certified to the ONC health IT certification criteria at 45 CFR 170.315.

What is EHR-based MIPS reporting?

EHR-based MIPS reporting is the direct submission of MIPS data from a Certified EHR (CEHRT) to CMS. The practice keeps quality data inside one system, from point of capture through final submission. No third-party intermediary handles the file and reporting responsibility stays with the clinician and the certified EHR.

EHR reporting is one of several reporting methods available for the 2026 performance year. The others are the Qualified Registry, a Qualified Clinical Data Registry (QCDR), and Medicare Part B claims measures. Medicare Part B claims measures are limited to small practices of 15 or fewer clinicians.

EHR reporting fits practices that:

• Run one certified EHR across the whole tax identification number (TIN)
• Want direct control of the data submitted to CMS
• Already capture eCQM, Promoting Interoperability and Improvement Activities data in structured fields
• Prefer to avoid third-party intermediary fees and submission timelines

The CMS Web Interface no longer appears in that list. CMS retired the CMS Web Interface as a quality collection type beginning with the 2025 performance year. Older MIPS guides that still name five reporting methods are out of date.

What is Certified EHR Technology (CEHRT)?

Certified EHR Technology (CEHRT) is electronic health record software certified under the ONC Health IT Certification Program. For the 2026 performance year, CEHRT functionality must meet the ONC health IT certification criteria at 45 CFR 170.315.

CMS retired the yearly edition naming convention. The CY2024 Physician Fee Schedule final rule aligned the Base EHR definition with the ONC HTI-1 rule. The 2015 Edition Cures Update label gave way to a single, edition-less criteria set at 45 CFR 170.315.

CEHRT does two jobs in MIPS:

• Promoting Interoperability cannot be scored without CEHRT, whatever the submission path
• Quality reporting through eCQMs requires the CMS EHR Certification ID from the Certified Health IT Product List (CHPL)

Which MIPS categories can you report through an EHR?

Three of the four MIPS performance categories move through the certified EHR. The fourth is calculated by CMS with no practice action.

Performance Category	Reportable Through the EHR?	How the Data Moves	2026 Weight
Quality	Yes, as eCQMs	QRDA III file generated by the CEHRT	30%
Promoting Interoperability	Yes, and CEHRT is required	Measure numerators, denominators and attestations	25%
Improvement Activities	Yes, by attestation	Yes or No attestation per activity	15%
Cost	No	CMS calculates from Medicare Part B claims	30%

One submission can carry all three reportable categories. Cost accounts for 30% of the final score without a single submitted record.

Can you report the Cost category through your EHR?

No. The Cost category is never submitted through an EHR, or through any other reporting method. CMS calculates Cost automatically from Medicare Part B claims already on file. Through the certified EHR, the practice submits Quality, Promoting Interoperability and Improvement Activities only.

How does EHR reporting fit into the MIPS reporting methods?

EHR reporting is one of several MIPS reporting methods, and the reporting-methods hub compares each one. The method chosen changes which measures are available and how each measure scores. The same clinical performance can score differently by collection type.

Method choice is not all-or-nothing. A practice can combine collection types inside the Quality category, reporting some measures as eCQMs and others through a registry. CMS scores each submission received and keeps the highest result.

What the method decides:

• Which quality measures are available to report
• Which benchmark each measure scores against
• Who holds responsibility for validating the file before submission
• Whether the practice pays a third-party intermediary fee

Compare the full set of options on the MIPS reporting methods hub before locking a submission plan for 2026.

How does EHR-based MIPS reporting work?

EHR-based MIPS reporting runs on a four-step workflow inside the certified EHR. Configuration happens before the performance period. Capture runs across the performance period. Export and submission happen after the performance period closes.

Each step depends on the one before it. An EHR that is not certified by the last day of the performance period cannot produce a scoreable file. Measures that were never mapped will not populate the export.

2026 timeline anchors:

• Quality performance period: January 1 to December 31, 2026
• Last start date for a 180-day Promoting Interoperability period: July 5, 2026
• Submission window: January 4 to March 31, 2027

CEHRT Configuration and Measure Mapping

Step 1 confirms the EHR meets the ONC health IT certification criteria at 45 CFR 170.315. The practice then maps each selected eCQM to the structured fields that feed it. Promoting Interoperability measures and Improvement Activities are configured in the same pass. Unmapped fields produce empty numerators at export.

Data Capture During the Performance Year

Step 2 runs the length of the performance period. The CEHRT captures eCQM data as clinicians document care in structured fields. Free-text documentation does not count toward an eCQM numerator. Monthly measure reports catch capture drift while the data set is still open.

QRDA III File Generation

Step 3 exports the aggregated results as a QRDA III file. QRDA III is the CMS Quality Reporting Document Architecture Category III standard for aggregate MIPS data. The file carries measure results at the TIN or TIN/NPI level, not patient-level detail. The 2026 CMS QRDA III Eligible Clinicians Implementation Guide governs the format.

Direct Submission to CMS (File Upload or API)

Step 4 delivers the file to CMS between January 4 and March 31, 2027. The practice signs in to qpp.cms.gov and uploads the QRDA III file. Direct API submission is a separate path, performed by an authorized third-party intermediary or health IT vendor. CMS scores every submission received and applies the highest score.

What are the direct submission requirements?

Direct submission carries requirements across four areas, and each one is checked before a score is issued. Three concern the technology and the file. One concerns the volume of data behind each quality measure.

Requirement	2026 Standard	Applies To
EHR certification	ONC health IT certification criteria, 45 CFR 170.315	Quality (eCQM), Promoting Interoperability
Certification identifier	CMS EHR Certification ID from the CHPL	Quality (eCQM), Promoting Interoperability
File format	QRDA III, per the 2026 CMS QRDA III EC Implementation Guide	Quality, Promoting Interoperability, Improvement Activities
Quality performance period	12 months, January 1 to December 31, 2026	Quality
Promoting Interoperability period	Minimum 180 continuous days in 2026	Promoting Interoperability
Improvement Activities period	Minimum 90 continuous days in 2026	Improvement Activities
Data completeness	75% of eligible encounters, all payers	Quality
Case minimum	20 eligible cases for benchmark scoring	Quality

A miss on certification or on the CMS EHR Certification ID zeroes the Promoting Interoperability category outright.

CEHRT Certified to ONC Criteria (45 CFR 170.315)

The EHR must have certified functionality in place on the first day of the performance period. Certification must be complete by the last day of that period. Submission also requires the CMS EHR Certification ID, generated on the Certified Health IT Product List (CHPL).

QRDA III Format

MIPS data leaves the EHR as a QRDA III extensible markup language (XML) file. The 2026 CMS QRDA III Eligible Clinicians Implementation Guide, version 1.1, sets the conformance rules. Files that fail the CMS Schematron validation are rejected before scoring.

Performance Periods (Quality 12 Months / PI 180 Days / IA 90 Days)

Each category carries a different minimum data window in 2026. Quality runs the full calendar year, January 1 to December 31, 2026. Promoting Interoperability requires a minimum of 180 continuous days, making July 5, 2026 the last possible start date. Improvement Activities require a minimum of 90 continuous days.

Data Completeness (75% Threshold)

Quality measures submitted as eCQMs must report on at least 75% of eligible encounters. The 75% threshold counts patients across all payers, not Medicare patients alone. CMS holds the threshold at 75% through the 2028 performance year. A measure below 75% scores minimal points.

Does your EHR still need 2015 Edition Cures Update certification for 2026?

Not under that name. CMS retired the edition naming convention starting with the 2024 performance year. The requirement for 2026 is CEHRT functionality meeting the ONC health IT certification criteria at 45 CFR 170.315. Products previously certified to the 2015 Edition Cures Update criteria were folded into that single criteria set. An EHR that never made the update cannot be scored for Promoting Interoperability.

How do you meet Promoting Interoperability (PI) through your EHR?

Promoting Interoperability is the MIPS category that requires a Certified EHR, so the EHR method is the natural fit. Promoting Interoperability carries 25% of the final score in 2026 for most participants.

The category covers five objectives. Those objectives are Electronic Prescribing, Health Information Exchange, Provider to Patient Exchange, Public Health and Clinical Data Exchange, and Protect Patient Health Information. Six or seven measures are required, depending on the Health Information Exchange option selected.

Four attestations gate the category in 2026:

• Security Risk Analysis, now carrying a second attestation on security risk management
• Annual self-assessment against the 2025 High Priority Practices SAFER Guide
• Actions to Limit or Restrict Interoperability of CEHRT
• ONC Direct Review

A “No” response on any of these attestations scores the entire category at zero. Measure-level requirements and scoring sit on the Promoting Interoperability category page.

When should you use Registry reporting instead of an EHR?

A Qualified Registry is a done-for-you alternative when a third party should validate and submit the data. The registry collects MIPS CQM data from the practice, applies current CMS specifications, and submits on the practice’s behalf.

Many registries pull directly from the EHR, which is where the confusion starts. A registry submission is not an EHR submission. The collection type changes from eCQM to MIPS CQM, and the benchmark changes with it.

Choose a registry when:

• The EHR is not certified, or certification lapses mid-year
• Needed measures exist as MIPS CQMs but not as eCQMs
• Clinicians span multiple EHRs under one TIN
• Data validation should sit with a vendor rather than the practice

Registry mechanics and vendor selection sit on the MIPS registry reporting page.

When should you use a QCDR instead of an EHR?

A Qualified Clinical Data Registry (QCDR) is the choice when specialty or non-MIPS measures are needed that an EHR cannot report. A QCDR develops and maintains its own measures, approved by CMS each year.

That measures inventory is the difference. QCDR measures are built for specialty workflows where the standard MIPS measure sets scores poorly or does not apply. Surgical, interventional and behavioral health specialties use QCDRs most heavily.

Choose a QCDR when:

• Specialty measures outperform the general MIPS measure set
• The EHR cannot produce the measures the specialty actually needs
• Benchmarks on available eCQMs are topped out and score poorly

Approval status and measure inventories sit on the QCDR MIPS reporting page.

Which EHRs support direct MIPS submission?

Most major certified EHRs support direct MIPS submission, including Epic, athenahealth, eClinicalWorks, Kareo/Tebra and Allscripts. Support means the EHR can generate a conformant QRDA III file for upload to qpp.cms.gov. Certification status is verifiable on the Certified Health IT Product List (CHPL).

One distinction matters at submission time. Uploading a QRDA III file is something the practice does directly.

An EHR vendor can only submit through the API on a practice’s behalf if that vendor is a CMS-approved third-party intermediary.

Vendor-specific configuration steps sit on the MIPS reporting by EHR software pages.

Is a Certified EHR required to report MIPS?

Not for every category. MIPS data can reach CMS through a Qualified Registry, a QCDR, or Medicare Part B claims, with no direct EHR submission involved. The Promoting Interoperability category is the exception. Promoting Interoperability requires Certified EHR Technology (CEHRT) regardless of submission method, because the category measures use of a certified EHR.

A practice without CEHRT can still report Quality and Improvement Activities. Promoting Interoperability then scores zero unless the practice qualifies for automatic reweighting or an approved hardship exception. Small practices, hospital-based clinicians, ASC-based clinicians and non-patient-facing clinicians receive automatic reweighting.

How does Macralytics set up EHR-based MIPS reporting?

Macralytics connects a certified EHR to CMS for direct MIPS submission. Work runs in four stages across the performance year.

1. Confirm the EHR meets the ONC health IT certification criteria at 45 CFR 170.315 and pull the CMS EHR Certification ID from the CHPL.
2. Map eCQM, Promoting Interoperability and Improvement Activities data to the structured fields that feed each measure.
3. Generate the QRDA III file and validate it against the 2026 CMS Schematron before the submission window opens.
4. Submit through qpp.cms.gov and confirm acceptance in the submission record.

Scope and timelines for the setup and validation work sit on the EHR integration for MIPS page.

Reporting MIPS through a Certified EHR (CEHRT) puts Quality, Promoting Interoperability and Improvement Activities into one workflow. That workflow ends with a QRDA III file submitted to CMS. Cost stays claims-calculated. The method suits practices running one certified EHR that want direct control of the file. A Qualified Registry or QCDR fits better where measure availability or validation capacity is the constraint. Compare each option on the MIPS reporting methods hub before the 2026 submission window opens.