CMS Encounter Data Submission Deadlines: A Plan-Side Reference

The CMS encounter data submission process is the mechanism by which Medicare Advantage plans report the diagnoses they want included in risk-adjusted payment. Most coders never see this side of the operation, but understanding the deadlines and the cutoff dates is essential for anyone working in risk adjustment — late or missing submissions are a top-three cause of lost RAF dollars, and the submission cutoff is what determines whether a chart found in retrospective review actually counts toward this year's payment.

This guide is a plain-English reference for how the EDS pipeline works, the key deadlines for each payment year, and the practical implications for coding teams trying to make sure their work translates into payment.

How the Encounter Data Pipeline Works

CMS pays Medicare Advantage plans on a per-member-per-month basis, with each member's payment adjusted by a Risk Adjustment Factor (RAF) score. The RAF is calculated from diagnoses reported during a 12-month data collection period. To get a diagnosis included in a member's RAF, the plan must submit it through one of two channels:

Channel 1 — Encounter Data System (EDS). Every claim a Medicare Advantage plan receives from a provider is forwarded to CMS as an encounter record. EDS submissions look like X12 837 claim files and are processed daily. CMS uses these to validate that the plan is actually paying providers for real services, and the diagnoses on the encounters are used for risk adjustment.

Channel 2 — Risk Adjustment Processing System (RAPS) supplemental files. Plans can also submit a separate "chart review" file that includes diagnoses found by retrospective coding teams that were not on the original claim. These are commonly used to capture diagnoses that the provider did not put on the bill but did document in the medical record.

CMS uses both sources to compute the final RAF for each member. The diagnoses that count are the ones that show up in either channel before the cutoff date for that payment year.

The Three Key Cutoff Dates

For each payment year, CMS publishes a series of deadlines that plans must hit to have diagnoses included in payment. The three that matter most:

1. Initial run cutoff — early in the calendar year following the data collection period. CMS runs an initial RAF calculation using all encounter and chart-review data submitted by this date. Plans receive a preliminary payment based on this run. Historically this cutoff has been in early March, though exact dates vary year to year.

2. Mid-year reconciliation cutoff — typically in the summer following the data collection period. CMS runs a mid-year reconciliation that picks up any diagnoses submitted between the initial cutoff and this date. Plans receive an adjustment payment (positive or negative) based on the new RAF. This is the last chance to add diagnoses that affect the current payment year for most plans.

3. Final reconciliation cutoff — typically in early January, roughly one year after the data collection period closed. CMS runs the final reconciliation. After this date, the data collection period for that payment year is closed and no further diagnoses can be added. This is the absolute final deadline.

The exact dates change every year and are published in the CMS Health Plan Management System (HPMS) memos. Plans should not memorize fixed dates; they should subscribe to HPMS notifications and put the published dates on the operations calendar.

What "Submitted by" Actually Means

CMS counts a diagnosis as submitted when the encounter or chart-review file containing it has been accepted into EDS or RAPS without errors. A file that is rejected does not count. A file that is in pending status does not count. A diagnosis on a provider claim that has not yet been adjudicated and forwarded does not count.

This matters because the practical submission deadline for coding teams is several weeks earlier than the published CMS cutoff. The plan needs time to:

A typical plan operates with a 2- to 4-week internal buffer before each CMS cutoff. Coding teams that try to push work right up to the published date often miss the cutoff because of file rejections or transmission delays.

How the Cutoffs Affect Coding Work

The three CMS cutoffs translate into three distinct internal deadlines for risk adjustment coding teams:

Pre-initial-run (typically December–February). Most retrospective chart review for the prior year's dates of service should be done by this point. Charts coded after this cutoff still count for the mid-year reconciliation, but plans prefer to capture as much RAF as possible in the initial run because the cash flow benefit is larger.

Pre-mid-year-reconciliation (typically May–June). The last big push for retrospective chart review. Plans typically run a final sweep of high-RAF members in this window and submit any newly discovered HCCs through chart review supplemental files.

Pre-final-reconciliation (typically October–December). Cleanup window. Plans use this period to fix rejected encounters, resubmit corrected files, and capture any remaining diagnoses from late-arriving claims.

What Happens to Late Diagnoses

A diagnosis that is documented in a 2025 encounter but is not submitted to CMS until after the final reconciliation cutoff for payment year 2026 does not affect 2026 payment. It is essentially lost RAF for that payment year. Plans cannot retroactively add it to a closed payment year, even if the documentation is solid and the chart would have passed any audit.

This is why timely chart review matters so much. The financial impact of a missed cutoff is permanent — those diagnoses are not just delayed, they are gone.

EDS vs RAPS: The Transition

For payment year 2025 and beyond, CMS pays Medicare Advantage plans entirely on EDS-based RAF calculations. The transition from RAPS-based payment was phased in over several years and is now complete for new payment calculations. Chart review supplemental files are still allowed and are still important — they are the primary way plans submit diagnoses found by retrospective coders that were not on the original provider claim — but the underlying payment system is EDS.

The practical implication for coding teams: chart review work is now most valuable when it can be tied to a specific encounter date that already exists in EDS. A diagnosis submitted via chart review supplemental file must reference a real encounter that was already submitted to CMS. This is sometimes called "linked chart review" and it requires coordination between the chart review team and the encounter submission team.

How to Audit Your Plan's Submission Performance

Coding leads who want to verify that their work is actually translating into payment should request three reports from the EDS submission team on a monthly basis:

1. Submission acceptance rate. What percentage of encounter and supplemental files submitted in the last 30 days were accepted by CMS without errors? Anything below 95% indicates a file format or data quality issue that is silently losing RAF.

2. Rejection reason breakdown. For rejected records, what are the top reasons? Common causes include invalid provider NPIs, mismatched member IDs, dates of service outside the data collection period, and invalid diagnosis codes (typically codes that were retired or codes that do not exist in the CMS valid diagnosis list).

3. RAF capture by source. What percentage of the plan's total submitted RAF came from encounter data vs chart review supplemental files? A healthy mix is roughly 70–85% from encounter data and 15–30% from chart review. Plans that are heavily dependent on chart review are at higher RADV risk because chart review diagnoses receive more scrutiny in audits.

The Bottom Line

Encounter data submission is the unglamorous part of risk adjustment, but it is the part that determines whether a coder's work actually turns into revenue for the plan. Coders who understand the cutoff dates, the difference between EDS and supplemental submissions, and the internal lead time required to clear pre-submission validation are significantly more effective at protecting RAF than coders who only look at chart-level documentation.

Every coding team should know its plan's three internal deadlines for the current payment year. If you do not know yours, ask. The cost of missing a cutoff is permanent — and almost always preventable.