Effective 340B compliance software does one thing most audit prep workflows don’t. It keeps covered entities ready before the audit notice arrives, not after.

HRSA conducts annual compliance audits of covered entities, and in FY 2025, 49% of audited programs received adverse findings. For most pharmacy teams, an audit notice triggers a separate workstream layered on top of an already stretched operation.

Documents get pulled. Data gets reconciled. Staff get redirected from patient care. The compliance gaps that created the risk in the first place are still there.

Programs built around continuous compliance (where documentation is current, transactions are verified, and OPAIS is synced daily) don’t face that scramble. 340BCheck is designed around exactly that approach.

The Three Findings That Keep Showing Up

HRSA’s audit process focuses on the same compliance pressure points year after year. Three categories account for the overwhelming majority of adverse findings.

Incorrect Office of Pharmacy Affairs Information System (OPAIS) records are the most persistent problem. OPAIS errors accounted for 62% of all audit findings in FY 2024, and in FY 2025 they appeared in three quarters of covered entities with adverse findings. HRSA uses OPAIS to validate transaction eligibility, so a stale or inaccurate record can make a compliant transaction appear improper.

Duplicate discounts tied to Medicaid Exclusion File (MEF) errors are the second recurring issue. In FY 2024, 91% of duplicate discount findings traced back to an inaccurate or incomplete MEF. Even one missing billing number can expose large volumes of claims.

Diversion at contract pharmacies rounds out the top three. In FY 2024, 82% of diversion findings involved 340B drugs dispensed at contract pharmacies for prescriptions written at ineligible sites. HRSA treats those prescriptions as categorically ineligible regardless of intent. Covered entities with the same diversion finding across two or more audits risk removal from the program.

The Rules Are the Same. The Risk Surface Isn’t.

HRSA’s core audit criteria have not changed. What has changed is the environment they apply to, and that environment is meaningfully more complex than it was five years ago.

• Contract pharmacy growth: Each contract pharmacy location is an additional compliance surface requiring monitoring for patient eligibility, prescriber site registration, and transaction accuracy. Managing that across a growing network of arrangements is difficult to sustain manually.
• Post-Loper Bright manufacturer restrictions: Following the Supreme Court’s 2024 decision, manufacturers have stronger legal standing to restrict contract pharmacy access. The practical requirements for participating covered entities can shift faster than manual processes can track.
• State-level regulatory variation: Dozens of states have enacted or introduced laws responding to manufacturer restrictions on 340B drugs. Health systems that operate across state lines now manage a patchwork of requirements on top of federal HRSA obligations.
• Program volume: In 2024, 340B covered entity purchases totaled $81.4 billion, a 23% increase from the prior year. More transactions mean more opportunities for eligibility errors, MEF mismatches, and OPAIS gaps to accumulate undetected.

What an Auditor Pulls on Day One

An HRSA audit follows a defined review process. The documentation it requires is consistent and predictable. Programs that maintain that documentation continuously have nothing to assemble under pressure.

Auditors review and verify:

• OPAIS accuracy: all registered sites, contract pharmacies, child sites, and entity-owned pharmacies must carry current names, addresses, and Medicare Cost Report data
• Internal controls: how the covered entity defines inpatient vs. outpatient status, how MEF designations are managed, and what procedures exist to prevent diversion and duplicate discounts
• Policies and procedures: written P&P documents must reflect current practice, not a prior compliance cycle
• Pharmacy service agreements: contract pharmacy oversight must document how patient eligibility is determined at each pharmacy and how dispensing, purchasing, and billing records are reconciled
• Transaction records: auditors test 340B drug transactions on a sample or judgmental basis across patient, provider, and location
• Remote audit protocols: for remote reviews, auditors use secure workspaces and encrypted communications; the scope mirrors an in-person audit

Every item on that list is something a well-configured compliance system maintains automatically.

340B Program Management That Runs in the Background

For pharmacy teams already managing dispensing operations, patient care workflows, and regulatory reporting, adding a compliance layer on top is not sustainable.

The answer isn’t more staff hours. It’s 340B compliance software built to integrate into the workflows that are already running.

Daily OPAIS Synchronization

OPAIS records must reflect the current reality: active contract pharmacy locations, accurate Medicare Cost Report dates, and no terminated sites left on the registry. Manual maintenance breaks down when staff turnover or operational changes create gaps between what OPAIS shows and what is actually true.

340BCheck syncs with OPAIS daily and flags mismatches as they occur, so discrepancies surface in days, not when an auditor requests documentation.

100% Transaction Auditing

Sampling a fraction of 340B transactions leaves the majority unreviewed. Automated auditing verifies every transaction across patient, provider, and location, then surfaces only the exceptions that require attention.

That coverage directly closes the gaps that produce diversion and duplicate discount findings: unregistered prescriber sites, MEF misalignments, and contract pharmacy eligibility errors.

Centralized Documentation Management

HRSA auditors review policies and procedures, pharmacy service agreements, and MEF designations as part of every audit. 340BCheck centralizes all of that documentation alongside transactional data, keeping it current and accessible rather than distributed across shared folders from prior compliance cycles.

Team Accountability and Task Management

Compliance gaps often trace back to accountability gaps, not data gaps. When multiple departments touch 340B operations, documentation responsibilities fall through the cracks. Workflow tools that assign tasks, set deadlines, and track follow-ups keep the right people responsible for the right items, without requiring pharmacy leadership to manually coordinate every update.

Run the Audit Before HRSA Does

Continuous monitoring reduces ongoing risk, but a periodic mock audit stress-tests whether documentation would hold up under actual scrutiny. Mock audit workflows within 340B compliance software simulate HRSA’s review process, giving compliance teams a chance to identify and close gaps before an auditor arrives.

HRSA’s self-disclosure process also allows covered entities to report and correct compliance issues proactively. Addressing a gap through self-disclosure is preferable to entering a Corrective Action Plan (CAP) process triggered by an adverse finding. CAP resolution is expected within six months of approval, and entities that miss that window risk termination from the program.

The Difference Between Reactive and Ready

Two covered entities can run the same 340B Drug Pricing Program and face very different audit outcomes, depending on how their compliance posture is built.

A documented, verifiable program is not the same as a perfect one. HRSA auditors follow a defined process, and covered entities that mirror that process internally don’t need to treat an audit notification as an emergency.

Most pharmacy compliance teams already know where their documentation is thin. The question is whether those gaps surface internally on their own timeline, or when an auditor requests a record that hasn’t been updated in two years. 340BCheck addresses the specific findings HRSA looks for:

• Daily OPAIS synchronization
• 100% transaction coverage
• Centralized documentation and pharmacy service agreements
• Mock audit workflows designed to hold up under scrutiny

Request a demo to see how covered entities are using it to stay audit-ready without disrupting the operations that keep patients served.