Epic and Cerner Integration Guide: HL7 & FHIR Connectivity Explained

Epic and Cerner (now Oracle Health)together account for more than 50% of the US inpatient EHR market. If you are building a healthcare application, integrating a medical device, or connecting any system to a hospital's clinical infrastructure, there is a very high probability you will need to integrate with one — or both — of these platforms.

In this guide, we cover everything you need to know about integrating with Epic and Cerner: their HL7 v2 interface capabilities, FHIR R4 APIs, proprietary integration points, and practical tips from our team's experience building EHR integrations across hundreds of healthcare organizations.

Epic HL7 Integration

Epic has been deploying HL7 v2 interfaces since the early 2000s and has extensive support for inbound and outbound HL7 messaging. Epic's interface engine (Bridges) manages all incoming and outgoing HL7 traffic and is highly configurable.

Epic HL7 Inbound Interfaces

Epic accepts inbound HL7 messages for a wide range of clinical workflows:

• ADT (A01, A03, A04, A08, A11, A28, A31) — Registration and patient demographic feeds from registration systems, bed management solutions, or third-party ADT sources.
• ORM/OML — Lab and radiology orders from Epic routed to ancillary systems, or orders from external systems loaded into Epic.
• ORU R01 — Lab results, radiology reports, and other clinical observations returned to Epic from ancillary systems. This is one of the most common Epic integration patterns.
• MDM T02 — Transcription and documentation from third-party dictation or documentation systems.
• VXU V04 — Immunization records from state registries or third-party immunization management systems.
• DFT P03 — Charge capture messages from ancillary systems into Epic's billing module.

Epic Interface Considerations

Epic's HL7 implementation uses many non-standard Z-segments to carry Epic-specific data (Epic CSN, encounter numbers, provider IDs, etc.). When building interfaces to Epic, your HL7 transformation logicmust account for these custom segments. Epic's integration team will provide an Interface Specification Document (ISD) detailing exactly what they expect.

Epic uses MLLP over TCP/IP for most HL7 v2 connections. Connections are typically managed by Epic's Bridges engine, and your integration engine (such as Mirth Connect) connects to Epic's listeners.

Epic FHIR APIs

Epic was an early adopter of FHIR and operates one of the most mature FHIR ecosystems in healthcare via the Epic App Orchard and its open.epic.com developer portal.

Epic FHIR Capabilities

• FHIR R4 (and R3) — Epic supports FHIR R4 for most data access scenarios, with some R3 (DSTU2) endpoints still available for legacy app compatibility.
• SMART on FHIR — Epic uses the SMART on FHIR authorization framework for all third-party app access. Apps must be registered and approved in the App Orchard (or via a site-specific registration for non-public apps).
• US Core Profiles — Epic's FHIR implementation follows US Core Implementation Guide profiles, supporting Patient, Observation, Condition, MedicationRequest, AllergyIntolerance, Immunization, and many other resources.
• MyChart Integration — FHIR APIs power patient-facing MyChart integrations, including patient data access, appointment scheduling, and messaging.
• Bulk FHIR — Epic supports the FHIR Bulk Data Access (Flat FHIR) specification for large-scale data exports — useful for analytics, population health, and payer-provider data exchange.

Getting Started with Epic FHIR

Development and testing can begin immediately at open.epic.com using Epic's sandbox environment. For production access, your application must be registered with Epic (either through the App Orchard for multi-site apps, or through direct customer activation for site-specific builds). Epic customers control which external apps can access their FHIR endpoint.

Cerner (Oracle Health) HL7 Integration

Cerner, rebranded as Oracle Health following its 2022 acquisition by Oracle, is the second-largest EHR platform in the US and has a substantial international presence. Cerner's integration architecture uses its Cerner HealtheIntent platform and Cerner Millennium for core clinical workflows.

Cerner HL7 Interface Support

Cerner supports a comprehensive set of HL7 v2 message types:

• ADT messages — Cerner Millennium generates and consumes ADT messages for patient registration, admissions, discharges, and transfers. Cerner's ADT feed is widely used to drive downstream systems.
• ORU R01 — Results interfaces from lab and radiology analyzers into Cerner are among the most common Cerner integration types. Cerner's results routing is managed through its Discern Rules engine.
• ORM/OML — Order messages from Cerner to ancillary fulfillment systems (lab analyzers, radiology modalities, pharmacy systems).
• SIU S12/S13/S14/S15 — Scheduling messages for appointment notifications to external scheduling or patient engagement systems.
• MDM — Document and transcription routing to and from Cerner.

Cerner Interface Considerations

Like Epic, Cerner uses custom Z-segments extensively. Cerner's FIN (Financial Account Number) and MRN (Medical Record Number) handling, provider NPI mapping, and facility/location codes require careful mapping in your integration transformation logic. Cerner typically provides a Functional Design Document (FDD) to guide interface development.

Cerner FHIR APIs

Cerner operates its FHIR platform through fhir.cerner.com (now transitioning to Oracle Health branding). Cerner was also an early FHIR adopter and supports a mature FHIR R4 implementation.

• FHIR R4 Support — Cerner's primary FHIR implementation is R4, with R3 (DSTU3) still supported at some sites. Cerner follows US Core and Argonaut profiles.
• SMART on FHIR — Like Epic, Cerner uses SMART on FHIR for app authorization. Apps must be registered through the Cerner developer portal (code.cerner.com / Oracle Health developer portal).
• Cerner Ignite APIs — Cerner brands its FHIR and non-FHIR API layer as Ignite APIs, which includes both FHIR endpoints and Cerner-proprietary REST APIs for workflows not yet covered by FHIR standards.
• HealtheIntent Platform — For population health and analytics use cases, Cerner's HealtheIntent platform offers additional data access patterns beyond standard FHIR.

Epic vs Cerner Integration Comparison

Integration Checklist: Before You Start

Whether you are integrating with Epic or Cerner, completing this checklist before development begins will save significant time and cost:

• Obtain the Interface Specification Document (ISD/FDD) — Request the EHR vendor's specification document for the message types you need. This is non-negotiable.
• Identify your use case — Is this a real-time HL7 v2 clinical message interface, a FHIR API for patient data access, or both? Define scope clearly.
• Request a test/sandbox environment — Both Epic and Cerner offer test environments. Never develop against production.
• Map your data model — Create a field-level data mapping between your system's data model and the EHR's HL7 segments or FHIR resource profiles.
• Plan for Z-segments and custom fields — Budget time for custom segment handling — especially for Epic MSH-3, Epic CSN, and Cerner FIN/encounter mapping.
• Define acknowledgment handling — Determine how your system handles AA, AE, and AR acknowledgments. HL7 ACK failures need retry and alerting logic.
• HIPAA BAA — Ensure a Business Associate Agreement is in place before any PHI flows through your integration.
• Schedule go-live testing windows — EHR vendors and hospitals have specific processes for go-live. Plan for a parallel-run period with clinical validation.

Our team at Taction Software has completed 500+ EHR integration projects, including dozens of Epic and Cerner interfaces. Contact us to discuss your integration requirements and get a free architecture consultation.