How to Document Pharmacy Medication Therapy Management Consultations

A practical guide for pharmacists on documenting MTM encounters, comprehensive medication reviews, targeted medication reviews, medication action plans, CMS program requirements, and CPT billing codes 99605, 99606, and 99607.

Why MTM Documentation Requires Its Own Framework

Most pharmacists document dispensing activity every day without much friction. Verification logs, counseling acknowledgments, and refill records follow well-worn paths. Medication therapy management (MTM) documentation is a different category of work. It is a clinical encounter, not a transaction, and the documentation requirements that govern it reflect that distinction.

MTM services under the Centers for Medicare and Medicaid Services (CMS) Part D program require pharmacists to conduct structured, time-limited reviews of a patient's complete medication regimen, identify and resolve drug therapy problems (DTPs), communicate findings to prescribers, and provide patients with a written summary of the encounter and their action plan. Every one of those steps generates a documentation artifact, and every one of those artifacts has both clinical and reimbursement consequences.

The complexity compounds because MTM encounters span two fundamentally different service types, each with its own structure, billing code, and documentation standard. A comprehensive medication review (CMR) is a complete, interactive assessment of a patient's medications, health conditions, and therapeutic goals, typically conducted in real time with the patient present. A targeted medication review (TMR) is a focused review directed at a specific medication-related concern, often conducted without a real-time patient encounter. Conflating the documentation requirements for these two service types is one of the more common billing and compliance errors in pharmacy MTM practice.

This guide walks through each documentation component of an MTM program, from initial eligibility screening through CMR and TMR documentation, medication action plan (MAP) delivery, drug therapy problem resolution, prescriber communication, and billing code selection.

Eligibility and Enrollment Documentation

Before a pharmacist conducts any MTM service, the patient's eligibility for the program must be established and documented. Under CMS requirements, Part D sponsors must target MTM enrollment to beneficiaries who meet specific criteria: multiple chronic conditions, multiple Part D-covered medications, and likelihood of incurring high drug costs.

The eligibility record should document:

The beneficiary's Part D plan enrollment and the specific MTM program offered by that plan
The chronic conditions identified as qualifying conditions for the program (e.g., diabetes, heart failure, hypertension, dyslipidemia, COPD, bone disease, mental health conditions, and others as specified by the plan)
The number of Part D-covered medications meeting the plan's threshold for MTM eligibility
The enrollment method: opt-in versus automatic enrollment with opt-out opportunity

This documentation is administrative rather than clinical, but it anchors the encounter. A chart that shows a CMR was conducted but contains no enrollment documentation creates an audit exposure, particularly when a plan is asked to demonstrate that services were delivered to eligible beneficiaries.

Comprehensive Medication Review Documentation

The CMR is the centerpiece of the CMS MTM program. It must be interactive, meaning it occurs in real time with the patient or caregiver. It must be comprehensive, meaning it covers all medications the patient is taking, not just Part D-covered drugs. And it must produce a specific deliverable: a written personal medication list (PML) and a medication action plan (MAP) provided to the patient or caregiver.

Pre-Encounter Medication Reconciliation

Before the CMR encounter begins, the pharmacist should compile and reconcile the patient's medication list from all available sources: prescription claims data from the Part D plan, any other pharmacy dispensing records the patient has shared, the patient's own medication bottles or lists, and any medication records from the patient's physician.

Document the sources used for the pre-encounter medication reconciliation. This step matters not only for clinical accuracy but because the quality of the CMR is partially assessed by whether it is truly comprehensive. A CMR based only on Part D claims data for a patient who fills some prescriptions at a different pharmacy, purchases over-the-counter medications regularly, and takes herbal supplements is incomplete regardless of how thorough the encounter itself is.

The pre-encounter record should list every medication identified prior to the encounter, the source for each entry, and any discrepancies or gaps identified (e.g., a medication listed in claims data with no recent refills, suggesting possible non-adherence or discontinuation).

The CMR Encounter Note

The CMR encounter is documented as a clinical note, and SOAP-style structure works well for this encounter type.

Subjective: The patient's own description of their health status, current symptoms, medication-related concerns, adherence difficulties, and any recent changes in condition or treatment. Capture the patient's language where it is clinically relevant. A patient who says "I stop taking my water pill when I have to go out" is reporting a specific adherence behavior that the subjective section should record verbatim or close to it.

Objective: The medication list reviewed during the encounter, including all prescription medications (Part D and non-Part D), over-the-counter medications, vitamins, minerals, and herbal supplements. For each medication, document:

Drug name (generic preferred with brand noted if relevant to adherence or coverage)
Dose and dosing frequency
Indication (the condition being treated)
Prescribing provider
Patient-reported adherence, including missed doses and any self-directed dose adjustments
Current refill status

Assessment: The pharmacist's clinical analysis of the medication regimen. This section is where drug therapy problems are identified and documented. A DTP is a medication-related problem that interferes with or has the potential to interfere with desired patient outcomes. Common DTP categories include:

Unnecessary medication (no valid indication, duplicate therapy, therapeutic overlap)
Need for additional medication (untreated condition, preventive therapy gap)
Ineffective medication (wrong drug for the indication, dosage form barrier)
Dose too low (subtherapeutic for the patient's condition and goals)
Dose too high (excessive dose, drug accumulation, organ function changes)
Adverse drug reaction (ADR) (side effect, allergic reaction, drug-induced illness)
Drug-drug interaction or drug-disease interaction requiring clinical action
Adherence problem (patient unable or unwilling to take medication as prescribed)

Each DTP identified should be documented with the specific medication involved, the clinical basis for identifying the problem, the potential or actual impact on the patient's health, and the pharmacist's recommended resolution.

Plan: The actions proposed or taken to resolve each DTP, including any recommendations communicated to prescribers, patient education delivered, referrals made, and the patient's response to the plan.

Consider a fictional example: Margaret L., a 74-year-old Part D beneficiary enrolled in MTM due to six chronic conditions and eleven medications. During her CMR, the pharmacist identifies three DTPs. First, Margaret reports she stopped taking rosuvastatin three months ago because of muscle aches and never told her cardiologist; the claims data shows no refills since discontinuation. This is an adverse drug reaction that has led to an untreated lipid condition. Second, her medication list includes both metformin and glipizide, but she reports her A1c at her last visit was 9.1 percent despite adherence to both medications; this suggests possible dose optimization need or need for additional therapy. Third, she takes ibuprofen over the counter for knee pain three to four times per week, which the pharmacist identifies as a potential drug-disease interaction given her stage 3 chronic kidney disease. Each of these DTPs is documented in the assessment with the clinical reasoning, and the plan section specifies the pharmacist's recommended action for each.

Personal Medication List Documentation

The personal medication list is a required CMR deliverable. It must be written in plain language, not clinical shorthand, and provided to the patient or caregiver. The PML should include every medication reviewed, the dose, the purpose (in patient-accessible language), and any specific instructions that are important for the patient to know.

Document in the chart:

That the PML was created and provided to the patient
The date provided
The format (paper, electronic, portal message)
Whether the patient or caregiver acknowledged receipt

If the patient took the PML but expressed confusion about it, or if a caregiver received it rather than the patient, note that in the chart. The PML is a patient safety document as much as it is a CMS deliverable.

Medication Action Plan Documentation

The medication action plan is distinct from the personal medication list. While the PML tells the patient what they are taking and why, the MAP tells the patient what to do differently. It is action-oriented, specific, and prioritized.

The MAP should be documented in the chart with each action item listed explicitly:

The specific action (not "discuss with your doctor" but "ask Dr. Rivera at your appointment on March 15th about whether ibuprofen is safe for your kidneys, given your kidney function test results")
The patient's role in each action
Any pharmacist follow-up actions associated with the item
The patient's response: whether they understood the action, expressed willingness to take it, identified barriers

Document any actions the patient declined or modified. A patient who says "I'm not going to bring up the statin with my cardiologist because I've already decided I won't take it again" is communicating a clinical decision that has implications for care coordination. That needs to be in the chart.

Continuing the fictional example: Margaret's MAP includes three items. She will contact her cardiologist's office by the end of the week to report that she stopped rosuvastatin due to muscle aches and ask about alternative options. She will ask her primary care physician at her upcoming visit about whether her diabetes medications need adjustment given her recent A1c result. She will stop using ibuprofen and try acetaminophen as an alternative for knee pain, which the pharmacist recommends based on her renal function, and she will ask her provider about safer options if acetaminophen does not control her pain adequately. Each item in the chart includes Margaret's verbatim response: she agreed to call the cardiologist and agreed to raise the A1c question; she expressed reluctance about changing her ibuprofen use but said she would try.

Targeted Medication Review Documentation

A TMR is a review focused on a specific medication concern rather than a comprehensive assessment of the entire regimen. TMRs may be conducted without a real-time patient encounter, which means they can be completed through chart review, claims analysis, and any available clinical data, followed by communication with the patient or prescriber.

The TMR note should clearly document:

The specific focus of the review (e.g., a new prescription for an anticoagulant in a patient already on aspirin and an NSAID, a sudden increase in insulin usage suggesting control problems, a high-risk medication added since the last CMR)
The clinical data reviewed: relevant claims, lab values available to the pharmacist, medication history
The pharmacist's assessment of the concern
The action taken: prescriber notification, patient outreach, recommendation made
The outcome: prescriber response, patient response, or documentation that no response was received within the defined follow-up period

One common TMR scenario involves high-risk medication monitoring. A fictional example: Robert K., 81 years old, is identified through claims data as having filled a new prescription for zolpidem 10 mg from a hospitalist following a brief hospitalization. He is already in the plan's MTM program and his claims history shows he takes several CNS-active medications. The pharmacist conducts a TMR focused on fall risk and sedation burden. The note documents the specific medications reviewed (zolpidem, lorazepam prescribed by his psychiatrist, and cyclobenzaprine for back pain), the calculated anticholinergic burden and CNS sedation risk, and the recommendation sent to both the hospitalist and the primary care physician flagging the combination as high risk in a patient over 80, referencing the Beers Criteria for potentially inappropriate medications in older adults. The note documents that the hospitalist responded within 48 hours, discontinuing the zolpidem and recommending non-pharmacological sleep support.

Pharmacist-to-Prescriber Communication Documentation

Effective MTM depends on pharmacists communicating findings to prescribers. That communication must be documented with the same care as the clinical findings themselves.

Every prescriber communication generated through an MTM encounter should be documented with:

The date and method of communication (fax, phone call, secure message, EHR portal)
The prescriber or prescriber's staff member reached
The specific recommendation or finding communicated
The clinical basis for the recommendation (brief, not a repeat of the full encounter note)
The prescriber's response, or documentation that no response was received and what follow-up action was taken

Document communication attempts that did not receive a response. If the pharmacist sent a recommendation to a prescriber and received no reply, the documentation should reflect the attempts made and any escalation steps taken (e.g., phone follow-up after a faxed recommendation went unanswered for five business days).

Prescriber communication documentation serves multiple purposes. It demonstrates clinical coordination, supports the pharmacist's professional liability position, and creates a continuity record that the next clinician to review the chart can follow.

Billing Code Selection and Documentation

MTM services are billed under three CPT codes. The selection of the correct code depends on the type of service provided, the time spent, and whether the service was provided to a new or established patient.

CPT 99605 covers an MTM service for a new patient, including assessment and intervention, provided by a pharmacist, with the first 15 minutes of face-to-face interaction with patient, family member, or caregiver.

CPT 99606 covers the same service for an established patient, with the first 15 minutes of face-to-face interaction.

CPT 99607 is an add-on code for each additional 15 minutes of face-to-face MTM service, used in conjunction with 99605 or 99606 when the encounter exceeds the initial 15-minute unit.

For accurate billing, the documentation must support:

New vs. established patient status: The chart should clearly reflect whether this is the patient's first MTM encounter or a follow-up.
Time: The total face-to-face time spent must be documented. A note that says a CMR was completed but does not document the duration of the encounter creates a billing support problem. Document start and end time, or total encounter duration in minutes.
Face-to-face interaction: The note must confirm that the service involved direct interaction with the patient, family member, or caregiver. CMR encounters that are conducted face-to-face or via interactive video qualify; encounters that are conducted without any patient interaction are TMRs and billed differently under Part D program structures.
Service content: The documentation must substantiate that the service delivered meets the definition of an MTM encounter, not merely a brief medication counseling interaction.

A CMR conducted with a new patient over 35 minutes of face-to-face time would be billed as CPT 99605 (first 15 minutes) plus CPT 99607 (one additional 15-minute unit, covering the remaining 20 minutes). The documentation must support 35 minutes of face-to-face MTM service to justify both codes.

Note that CMS Part D MTM programs may have their own billing and submission requirements separate from CPT codes. Pharmacists providing MTM services through a Part D plan should confirm the plan's specific submission requirements, since some plans pay pharmacies directly through plan-specific billing mechanisms rather than through standard CPT submission.

Common Documentation Mistakes in MTM Practice

Documenting the PML and MAP as one document without distinguishing them. CMS requires both a personal medication list and a medication action plan as separate deliverables. A combined document that lists medications and includes action items may serve patients well clinically, but the chart should clearly identify both deliverables by name and confirm that both were provided.

Recording DTPs without clinical basis. Writing "patient taking too many medications" in the assessment section does not document a drug therapy problem. Each DTP requires the specific medication, the specific concern, and the clinical reasoning. "Rosuvastatin discontinued by patient due to self-reported myalgia; lipid management now unaddressed" is a documented DTP. The former is an observation; the latter is a clinical finding.

Failing to document prescriber communication attempts. Pharmacists often make the clinical recommendation and document it well but fail to document what happened next. If no response was received, that needs to be in the chart. An undocumented recommendation is clinically and legally equivalent to a recommendation that was never made.

Using CPT 99606 without confirming established patient status. The distinction between new (99605) and established (99606) patients matters for billing accuracy. If your documentation system does not clearly reflect prior MTM encounter history, it is easy to bill 99606 for patients who should be billed at 99605. Confirm your patient's MTM encounter history before finalizing billing.

Not documenting time for add-on code justification. The most consistently underperforming element of MTM billing documentation is time. If you are billing CPT 99607 because the encounter exceeded 15 minutes, the documentation must support the time claimed. "CMR completed" without a duration is not sufficient.

Documenting patient education without patient response. Noting that education was provided on medication adherence is less useful than documenting what the patient said in response, what they identified as their main barrier to adherence, and what they agreed to try. The latter supports clinical continuity; the former is a checkbox.

For pharmacists who structure CMRs using a consistent note format, tools like NotuDocs allow you to build a template that matches your MTM documentation workflow, so AI fills the pharmacist-defined fields from your own encounter notes rather than generating generic clinical language.

Drug Interaction and Adherence Documentation Examples

Two documentation scenarios come up frequently enough in MTM practice that they deserve specific attention.

Documenting Drug-Drug Interactions

When a pharmacist identifies a clinically significant drug-drug interaction, the note should document:

The specific interacting agents and the mechanism of the interaction
The potential clinical consequence (e.g., increased bleeding risk, QT prolongation, serotonin syndrome risk, reduced efficacy of one agent)
The patient's current symptom status relevant to the interaction
The pharmacist's recommendation and its basis
The urgency of the recommendation (routine follow-up versus urgent prescriber contact)

A fictional example: Sandra P., 68 years old, presents for her annual CMR. Her medication list includes warfarin 5 mg daily for atrial fibrillation and a new prescription for fluconazole 150 mg for a vaginal yeast infection prescribed by an urgent care provider. The pharmacist identifies a significant CYP2C9-mediated drug-drug interaction between fluconazole and warfarin, with fluconazole inhibiting warfarin metabolism and potentially causing a significant INR elevation. The note documents the specific mechanism, the clinical risk (bleeding), Sandra's current INR history, and the pharmacist's urgent outreach to both the urgent care provider and Sandra's anticoagulation clinic. It notes the recommendation to monitor INR within 3 to 5 days and consider dose reduction, and documents that Sandra was counseled to watch for signs of bleeding.

Documenting Adherence Assessments

Medication adherence documentation in MTM should go beyond a binary adherent/non-adherent classification. Useful adherence documentation captures:

The patient's self-reported adherence pattern for each medication
Any adherence aids in use (pill organizer, blister pack, caregiver assistance)
Identified barriers: cost, side effects, regimen complexity, cognitive or physical barriers, health beliefs
Objective adherence data where available (refill records showing proportion of days covered)
The pharmacist's clinical interpretation: is the adherence pattern likely to be affecting therapeutic outcomes?

Adherence barriers that are documented without a corresponding plan action are missed opportunities. If a patient cannot afford one of their medications and that is documented in the chart, the MAP should include a specific action item: exploring patient assistance programs, discussing therapeutic alternatives with the prescriber, or at minimum confirming that the patient and prescriber are aware of the cost barrier.

MTM Documentation Checklist

Eligibility and Enrollment

Part D plan MTM program eligibility criteria met and documented
Qualifying chronic conditions identified and listed
Number of qualifying Part D medications documented
Enrollment method documented (auto-enrollment vs. opt-in)

Pre-CMR Preparation

Medication list compiled from all available sources
Sources used for medication reconciliation documented
Discrepancies or gaps in claims vs. reported medications noted

CMR Encounter Note

Encounter date and duration (start and end time or total minutes) documented
New or established patient status confirmed
Subjective: patient-reported health status, symptoms, adherence concerns
Objective: complete medication list with dose, indication, prescriber, adherence status
Over-the-counter medications, vitamins, and supplements included
Assessment: each DTP identified with specific medication, clinical basis, and potential impact
Plan: proposed resolution for each DTP, patient response documented