5 ways Fivetran powers healthcare data integration

Healthcare data should power faster decisions and better patient outcomes — but fragmentation gets in the way. Clinical, operational, and financial data is spread across systems like Epic, EDI, and HL7, each with different formats and requirements. At the same time, strict regulations mean even small integration failures can carry real legal and operational consequences.

Fivetran was built for exactly that kind of complexity. Together, its pre-built Epic connector, file ingestion capabilities for HL7 and EDI, extensible Connector SDK for FHIR, and Hybrid Deployment capabilities address the 5 most common data integration challenges in healthcare without requiring your team to build and maintain fragile custom pipelines. Here's how each one works.

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1. Epic Clarity connector

Epic is the most dominant EHR platform in US healthcare, installed across more than 250 million patient records and used by 28 of the top 30 US hospitals. For clinical analytics, population health, and operational reporting, Epic is where the data lives. But extracting it has historically meant weeks of brittle custom SQL scripts, manual schema mapping, and ongoing maintenance every time Epic updates its data model.

Fivetran's Epic Clarity connector eliminates that by replicating Clarity (Epic's reporting database, built on SQL Server) directly to your destination — Snowflake, Databricks, BigQuery, or Redshift — using automated change data capture. Schema changes in Epic are detected and propagated automatically. The connector supports both SaaS and Hybrid deployment models, so organizations that can't route PHI through third-party networks have a compliant path forward.

2. HL7 file support

HL7 version 2 is the workhorse standard for real-time clinical messaging — patient admissions (ADT), lab results (ORU), medication orders (RDE), and surgical records all travel between hospitals, labs, and insurance companies as HL7 v2 files. These files are deceptively complex: unlike CSV, they use a pipe delimiter rather than a comma, and critically, records within a single file can be nested, requiring a two-level parse rather than a simple row-by-row read.

This technique is demonstrated in this technical blog series on ASCII file integration, Fivetran's file connectors — S3, FTP, SFTP, Google Drive — ingest HL7 files as-is and land them in the warehouse with their raw content intact. From there, SQL views parse each segment type (MSH, PID, PV1, OBX) using Snowflake's SPLIT and GET functions on the pipe delimiter. The late-binding approach means no upfront schema declaration is required, and the full HL7 message is always available for reprocessing as parsing logic evolves. Read the full technical walkthrough.

3. EDI support

EDI (Electronic Data Interchange) is the backbone of healthcare administration. Every claim, payment, and eligibility check between providers, payers, and clearinghouses travels as an EDI transaction. The X12 standard defines dozens of transaction types relevant to healthcare: 837 (medical claim submission), 835 (claim payment and remittance advice), 270/271 (eligibility inquiry and response), 278 (prior authorization request and response), and 276/277 (claim status inquiry and response). Each transaction type uses a different segment structure with asterisk delimiters and tilde record terminators — a format that predates the modern web and resists standard parsing tools.

This blog shows how Fivetran's file connectors handle EDI using the same late-binding ELT approach as HL7. Files land in the warehouse raw; SQL parsing logic then extracts each segment type into structured tables. Because the full EDI transaction is preserved in its original form, payers and providers can reparse historical transactions when business rules change — a capability that early-binding ETL solutions can't provide.

4. FHIR via the Connector SDK

FHIR (Fast Healthcare Interoperability Resources) is the modern standard for healthcare data exchange, mandated by the 21st Century Cures Act for all US EHR systems. Unlike HL7 v2 files or EDI transactions, FHIR uses RESTful APIs and JSON — a format that modern data tools understand natively. FHIR resources cover the full clinical domain: Patient, Observation, Condition, MedicationRequest, Encounter, DiagnosticReport, and dozens more, each representing a well-defined clinical entity with a standardized JSON schema.

Fivetran doesn't yet have a built-in FHIR connector, but the Connector SDK closes this gap rapidly, with a couple for review, like one public example here. The SDK's Python framework handles authentication, pagination, incremental state management, and schema mapping — exactly the plumbing required to build a FHIR connector. Because FHIR's RESTful structure is predictable and its JSON schemas are well-documented, a working connector that pulls Patient, Observation, and Encounter resources incrementally using the _lastUpdated search parameter can be written, tested, and deployed within 15 minutes. Once deployed, it runs on Fivetran's managed infrastructure with the same scheduling, monitoring, and schema evolution as any built-in connector.

5. Fivetran’s Hybrid Deployment

Healthcare data integration has a fundamental tension: modern analytics platforms are cloud-based, but HIPAA requires that Protected Health Information (PHI) be handled with strict controls over where it travels and who can access it. For many health systems, routing clinical data through a third-party cloud service — even an encrypted one — is a compliance and risk posture that legal and security teams won't approve. The traditional solution was to build entirely custom, self-managed pipelines that never left the internal network. The result was brittle infrastructure that consumed engineering time and introduced its own breach risks through manual maintenance.

Fivetran's Hybrid Deployment resolves this tension. A lightweight agent runs inside the organization's own VPC or on-premises infrastructure. Data is processed entirely within that environment — it never traverses Fivetran's cloud. The agent communicates with Fivetran's cloud control plane using outbound-only mutual TLS (mTLS), meaning no inbound firewall ports are required. Configuration, scheduling, monitoring, and alerting all happen through Fivetran's standard dashboard. The result is a fully managed pipeline experience with the security posture of an entirely self-hosted solution. Fivetran is HIPAA compliant, signs BAAs, holds HITRUST certification on its Business Critical plan, and maintains SOC 2, ISO 27001, and PCI DSS Level 1 certifications.

Fivetran makes integrating healthcare data straightforward

Epic, HL7, EDI, FHIR, and on-premises PHI are 5 of the hardest data integration problems in healthcare — and Fivetran has a specific, tested answer for each one. The outcome is a governed, analytics-ready data foundation that lets clinical and operational teams focus on insights, not infrastructure.

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