Medication Reconciliation

What is medication reconciliation?

Medication reconciliation is the structured comparison of a patient's medication lists from the EHR, pharmacy records and the patient's own report, followed by a clinician's decision on each drug: continue, change, stop or start. The result is one reviewed list that travels with the patient to the next setting of care.

In software terms, reconciliation is a merge with a human approver. The tool gathers candidate lists, proposes matches, shows the differences and records each decision with the clinician who made it.

Where does each medication list come from?

Each list comes from a different system with a different meaning, and the tool has to keep those meanings apart. Mixing an order, a fill and a patient statement into one undifferentiated list leads directly to reconciliation errors.

• EHR orders: Prescriptions and inpatient orders, exposed in FHIR as MedicationRequest. US Core profiles MedicationRequest and Medication, so it has a common FHIR profile across certified EHRs.
• Patient-reported medications: What the patient or family says is being taken, including over-the-counter products and supplements. FHIR R4 has MedicationStatement for this, but US Core does not profile it, so EHRs differ in how they expose it.
• Pharmacy fill and claims history: Surescripts describes its Medication History for Reconciliation product as deduplicated medication history from pharmacy benefit managers and pharmacies, delivered into the EHR workflow.
• Outside records: Medications sections in C-CDA documents received from other organizations, often through an HIE or a transition of care message.
• Inpatient administration: For discharge, the eMAR shows what was actually given in hospital, which can differ from the home list and the admission orders.

Fill and claims data show that a prescription was dispensed or paid for, not that the patient takes it. Over-the-counter products, samples and supplements bought outside a prescription will not appear in pharmacy claims at all.

Record the retrieval time and source system on every entry. A list pulled at registration may be hours or days old by discharge, and the clinician needs to see that before trusting it.

How does a reconciliation session run step by step?

A reconciliation session runs in six steps, from gathering lists to sending the result. The tool should make each step fast for the clinician without hiding any source.

• 1. Gather: Pull the EHR active list, the patient-reported list, the pharmacy history and any outside documents, and record when each was retrieved.
• 2. Normalize: Map each entry to a standard drug concept, usually RxNorm, and parse dose, route and frequency into structured fields where the source allows it.
• 3. Match: Group entries that refer to the same drug, flag near matches such as the same ingredient at a different dose, and list unmatched entries separately.
• 4. Review with the patient: Show the grouped list so the clinician can confirm what the patient actually takes, including doses taken differently from the label.
• 5. Decide: Record continue, change, stop or start for every entry, with a reason for each change or stop, and the clinician's identity and time.
• 6. Publish: Write the reconciled list back to the EHR, produce the patient's list in plain language, and include it in the summary of care sent to the next provider.

Discharge adds one more comparison: the home list from admission, the inpatient orders and the new prescriptions. Every home medication must end the session either resumed, changed or stopped, never simply missing.

How do two entries become one match?

Two entries become one match when they resolve to the same clinical drug concept, and the hard cases are the ones that resolve to related but different concepts. Matching rules decide how much the clinician has to read.

RxNorm, maintained by the US National Library of Medicine, gives normalized names and identifiers for clinical drugs and links brand and generic forms. A branded product and its generic map to related concepts, so the tool can group them even when one list says the brand and the other the generic.

• Exact concept match: Same ingredient, strength and dose form. Group automatically and show one line with both sources.
• Same ingredient, different strength: Group and highlight the difference. This may be a real dose change, or a patient taking two tablets of a lower strength.
• Same class, different drug: Do not group. Flag a possible duplicate therapy for the clinician instead.
• Combination products: Match on each ingredient so a combination tablet is not listed beside one of its components without a warning.
• Free text only: Show the text with no match and ask for coding, because uncoded entries cannot be checked for duplicates or interactions.

Keep the matching rules visible and testable. A clinician who sees two lines grouped wrongly once will stop trusting the grouping and review every line by hand.

Which rules ask for reconciliation?

Several CMS and accreditation requirements expect reconciliation at transitions of care. These are the ones a build team should know by citation.

• CMS Promoting Interoperability: The "support electronic referral loops by receiving and reconciling health information" measure for eligible hospitals and CAHs requires clinical information reconciliation for medication, medication allergy and current problem list using CEHRT (42 CFR 495.24(e)(6)(ii)(B)).
• Transitional care management: The CMS MLN Transitional Care Management Services booklet (August 2025) says medication reconciliation and management must be furnished on or before the date of the face-to-face visit.
• Joint Commission: National Performance Goals replaced the National Patient Safety Goals chapter for hospital and critical access hospital programs on 1 January 2026, and Medication Management is one of the goal topics.
• HIPAA: Medication lists and pharmacy history are ePHI, so the tool must meet the HIPAA Security Rule safeguards in 45 CFR Part 164 Subpart C, including audit controls and person or entity authentication.

Ask the quality team which measures and accreditation elements the organization reports. Those decide which fields, timestamps and audit records the tool must keep.

The Promoting Interoperability measure groups medication with medication allergy and current problem list. Design the decision record once so it serves all three reconciliations.

Where reconciliation tools fail clinicians

Reconciliation tools fail when they add clicks without adding certainty. This failure-point list covers the problems that push clinicians back to paper lists.

• Lost provenance: Entries from fill history, the patient and the EHR look identical, so the clinician cannot tell an order from a pharmacy claim.
• Stale history: The pharmacy history was pulled days earlier at registration and is shown as current at discharge.
• Bulk accept: A single button continues every medication, so the reconciliation is recorded but never actually done.
• Silent drops: A home medication with no match disappears from the discharge list instead of needing an explicit stop.
• No patient list: The tool produces a clinical list but no plain-language version, so the patient goes home without knowing what changed.
• One-way data: The reconciled list stays in the add-on tool and never reaches the EHR active list, so the next encounter starts from the old list.
• Free-text dosing: Sig text is stored unparsed, so a dose change looks like an exact match.

Each of these can be caught in usability testing with clinicians working through realistic, de-identified lists before go-live. Synthetic lists with tidy coding can hide them.

Writing the reconciled list back

Writing the list back needs a write path the EHR actually supports, which may not be the same API used to read it. Plan the write path before designing the screens.

The ASTP/ONC standardized API at 45 CFR 170.315(g)(10) is a read API for patient and population services. It does not let an outside app write medications into the EHR. A write needs the EHR vendor's own write APIs, an HL7 v2 interface such as pharmacy or order messages, or a workflow where the clinician signs the changes inside the EHR.

One workable pattern is a SMART on FHIR app that reads through FHIR, then hands the decisions to the EHR's native order and medication list screens for signing. That keeps orders inside the EHR's safety checks while the app handles gathering, matching and review.

Whichever path is chosen, keep the decision record in the tool as well: every source entry, the match, the decision, the reason and the signer. That record is what an audit or a safety review will ask for.

Test the write path with edge cases: a stopped drug the EHR still shows as active, a dose change that creates a new order, and a newly started drug that needs pharmacy verification.

How Agnotic can help

A reconciliation tool earns trust when every entry shows its source and every decision is recorded. Agnotic Technologies builds medication management software for hospitals and digital health companies, including reconciliation screens, medication history feeds, RxNorm matching and the EHR read and write paths behind them.

Agnotic connects FHIR MedicationRequest and patient-reported data, integrates pharmacy history, builds matching rules clinicians can test, and delivers the reconciled list back to the EHR through vendor APIs or HL7 v2 interfaces, with a full decision audit trail.

Sources

• 42 CFR 495.24: Promoting Interoperability objectives and measures
• CMS MLN: Transitional Care Management Services booklet (August 2025)
• The Joint Commission: National Performance Goals
• HL7 FHIR R4: MedicationStatement
• HL7 US Core: MedicationRequest profile
• Surescripts: Medication History for Reconciliation
• NLM: RxNorm
• 45 CFR 170.315: ONC certification criteria, including (g)(10)