How to Migrate Healthcare Data from HL7 to FHIR?

In healthcare, the ability to share data seamlessly across systems is absolutely crucial. For years, HL7 has been the go-to framework, helping organizations exchange vital information. But as the demand for real-time data and more connected systems increases, HL7 is increasingly being replaced by FHIR, as it offers a more flexible and faster solution, making it easier for healthcare providers to share patient data efficiently and securely.

For healthcare platforms looking to stay ahead in the digital age, migrating from HL7 to FHIR is no longer optional. It’s a necessary step to ensure smooth interoperability, improve patient care, and adapt to the rapidly changing healthcare landscape in 2025 and beyond.

Our team specializes in guiding organizations through the migration process, making sure all legacy systems are efficiently integrated and that your platform benefits from enhanced scalability and compliance with evolving healthcare regulations. In this blog, we’ll explore the steps required to migrate healthcare data from HL7 to FHIR, the benefits of making the switch, and how to ensure a seamless integration of FHIR for modern healthcare systems.

Key Market Takeaways for Healthcare Data Migration

According to MarketResearchFuture, the healthcare data interoperability market is experiencing significant growth, expected to jump from USD 68.96 billion in 2024 to USD 533.92 billion by 2034. This increase is fueled by the growing need for seamless data exchange, changing regulations, and the shift toward value-based care. As healthcare organizations strive to improve care delivery, the migration from legacy HL7 systems to the more modern FHIR standard is becoming a key focus.

Source: MarketResearchFuture

FHIR’s flexibility makes it a game-changer for healthcare providers. Its real-time, API-based access to patient data improves interoperability across different systems. The modular design of FHIR allows for easier integration with electronic health records, telemedicine platforms, and patient-facing apps, which enhances care coordination and engagement.

Industry leaders like Epic Systems and Cerner have already adopted FHIR-based APIs, enabling secure and efficient data exchange. In addition, major cloud providers such as Google Health and Microsoft Azure are supporting large-scale HL7 to FHIR migration projects, making it easier for healthcare organizations to transition to FHIR and unlock the potential for better patient outcomes and advanced analytics.

What is FHIR and Its Importance in Healthcare?

FHIR or Fast Healthcare Interoperability Resources, is a modern healthcare data standard developed by HL7 International to enable seamless sharing and exchange of EHRs across different systems. Unlike older healthcare data formats, FHIR is built on contemporary web technologies like RESTful APIs, JSON, and XML, making it much easier to integrate, access, and exchange healthcare data in real time.

FHIR organizes medical data into modular units called “Resources” (such as Patient, Observation, Medication, and Appointment). These can be combined to represent complex clinical workflows, ensuring that the system is flexible, scalable, and compatible with modern mobile and cloud-based healthcare applications.

FHIR vs. HL7: A Comparison

While HL7 v2 and v3 have long been essential in healthcare interoperability, they come with certain limitations that make them less suited for modern healthcare needs. Here’s a comparison:

Why FHIR is Better for Modern Healthcare?

• API-First Approach: FHIR uses standard RESTful APIs, making it easier for developers to integrate with EHRs, telehealth platforms, and analytics tools.
• Real-Time Data Exchange: Unlike HL7, which processes data in batches, FHIR allows instant data retrieval and updates, critical for emergency care and remote monitoring.
• Better for AI & Analytics: The structured, standardized nature of FHIR data simplifies machine learning, predictive analytics, and population health management.
• Regulatory Compliance: FHIR aligns with the Office of the National Coordinator’s interoperability rules, USCDI, and HIPAA, ensuring compliance with current healthcare regulations.

Why FHIR Matters in Enterprise Healthcare?

Healthcare systems today use a variety of platforms like EHRs, billing systems, and patient portals. Without interoperability, patient data is siloed, leading to inefficiencies and potential errors. FHIR solves this by enabling seamless, secure data sharing between providers, insurers, and patients.

Advantages Over Older Standards

FHIR’s modular structure offers great flexibility, allowing it to be customized for a variety of use cases like genomics and wearable devices. Its cloud-native design makes it scalable to support large healthcare enterprises, while its API-first approach simplifies implementation for developers, reducing both development time and costs.

Major Industry Adoption

Leading EHR vendors like Epic, Cerner, and Allscripts have embraced FHIR APIs for seamless data exchange, ensuring better interoperability across systems. Additionally, government mandates from CMS and ONC now require FHIR for payer-to-provider data exchanges, pushing the industry toward greater standardization. Big tech companies such as Google, Microsoft, and Apple are also leveraging FHIR to integrate and manage health data across their platforms, further accelerating its adoption.

Future-Proofing Healthcare IT

With the rise of AI-driven diagnostics, IoT wearables, and telehealth services, FHIR ensures that healthcare systems remain agile and adaptable. By adopting FHIR now, enterprises can:

• Reduce long-term integration costs.
• Improve patient engagement through APIs.
• Stay ahead of regulatory changes, keeping systems compliant with evolving standards.

Benefits of Migrating from HL7 to FHIR

 Shifting from HL7 to FHIR is transforming healthcare by making data exchange smoother and more efficient. FHIR offers cost savings, better integrations, and improved patient care. It’s a game-changer for healthcare providers, payers, and tech platforms looking to stay ahead in a fast-evolving industry.

Technical Advantages of FHIR

1. Improved Interoperability Between Disparate Systems

Traditional HL7 (v2/v3) relies on batch processing and custom interfaces, making real-time data exchange challenging.

FHIR Solution: FHIR uses standardized RESTful APIs, enabling seamless, real-time communication between EHRs, labs, pharmacies, and telehealth platforms. This reduces errors, eliminates data silos, and ensures that healthcare providers have access to up-to-date patient records, leading to better clinical outcomes.

2. Easier Integration with Modern Technologies

FHIR’s JSON/XML-based APIs work natively with cloud platforms (e.g., AWS, Azure, GCP) and mobile apps. The structured FHIR resources (e.g., Patient, Observation) simplify machine learning, predictive modeling, and population health analytics. FHIR supports continuous data feeds from remote monitoring devices, such as glucose monitors and fitness trackers, allowing for more comprehensive patient care.

3. Standardized Data Models for Better Accuracy

HL7 messages (e.g., ADT, ORU) often vary by vendor, requiring complex and custom parsing logic.

FHIR’s Consistency: FHIR’s predefined Resources (e.g., MedicationRequest, Condition) follow a uniform schema, reducing mapping errors and manual data cleanup. Built-in validation tools like FHIR Validator and Inferno help ensure data integrity and compliance, minimizing data quality issues.

Business Advantages of FHIR

1. Reduced Integration & Maintenance Costs

Legacy HL7 interfaces require costly middleware and ongoing maintenance, which can strain IT resources.

FHIR Savings:

• Fewer custom interfaces are needed, cutting development time by 30–50%.
• Cloud-hosted FHIR servers (e.g., Azure FHIR, Google Healthcare API) reduce infrastructure and maintenance costs, making it a cost-effective solution in the long run.

2. Enhanced Patient-Centered Care

FHIR aggregates data from multiple sources like EHRs, wearables, and patient portals, providing a single, comprehensive view of the patient. APIs enable FHIR-enabled apps (e.g., Apple Health Records) to share patient data securely.

Use Case: A diabetes patient’s glucose readings from a continuous glucose monitor (CGM) can automatically sync with their EHR, enabling healthcare providers to offer more proactive and personalized care.

3. Future-Proofing & Scalability

HL7 v2 is becoming obsolete as it lacks support for modern system architectures like microservices and serverless computing, which are crucial for scalable operations. In contrast, FHIR offers greater flexibility, scaling seamlessly for both large healthcare organizations and smaller startups. It also adapts easily to new regulations such as USCDI and TEFCA, ensuring long-term sustainability and compliance without the need for major system overhauls.

4. Competitive Advantage for FHIR-Compliant Platforms

• Market Demand: 90% of EHR vendors, including Epic and Cerner, now support FHIR. Non-adopters risk falling behind as the industry continues to embrace this standard.
• Partnership Opportunities: FHIR compliance unlocks integration possibilities with emerging health tech solutions, such as AI diagnostics and remote patient monitoring platforms.
• Regulatory Edge: Mandates like the CMS Interoperability Rule prioritize FHIR for payer-to-provider data exchange, positioning FHIR-compliant platforms ahead of regulatory requirements.
  

Steps for Migrating Healthcare Data from HL7 to FHIR

Our expertise lies in assisting healthcare organizations with efficient HL7 to FHIR migrations. We follow a precise, step-by-step approach to ensure a smooth process, maintaining data integrity and preparing your systems for future scalability.

1. Assess the Current HL7 Data Infrastructure

First, we thoroughly assess your existing HL7 infrastructure. We take the time to understand how your current system works and identify the specific data elements that need to be migrated. We then conduct a gap analysis to pinpoint where HL7 data differs from FHIR data, ensuring we know exactly what adjustments need to be made for a smooth transition.

2. Define FHIR Implementation Strategy

Next, we define the strategy for implementing FHIR in your system. We decide which FHIR resources, such as Patient, Observation, or Encounter, are most relevant to the healthcare data you’re migrating. Our team works to map your existing HL7 data to FHIR’s resources, ensuring the migration is as smooth as possible and that all necessary data is properly represented in the new system.

3. Choose the Right Tools and Frameworks

We carefully select the right tools and frameworks to facilitate the HL7 to FHIR migration process. This includes picking out the best conversion tools, integration platforms, and APIs that will help us efficiently migrate your data. Our team also identifies the middleware needed to ensure smooth communication between your old HL7 system and the new FHIR-based system during the transition.

4. Data Mapping and Transformation

Our experts map your HL7 data to the corresponding FHIR resources. Using data transformation tools, we ensure that the migration is done accurately, preserving the integrity of your healthcare data. We work closely with your team to verify that each data element is appropriately transformed and compatible with FHIR’s structure.

5. Implement Testing and Validation

Once the migration is in progress, we conduct rigorous testing to ensure that everything is working as it should. Our team validates the migrated data, checking for consistency, completeness, and compliance with FHIR standards. We test the system thoroughly to make sure your data is fully integrated and meets all required guidelines before going live.

6. Monitor and Optimize Post-Migration

After the migration is complete, we don’t just walk away. We set up monitoring systems to track data integrity and ensure your new FHIR system is running smoothly. We continuously optimize the integration, addressing any potential issues and ensuring your healthcare data remains accurate, secure, and efficient as your system evolves.

Common Challenges and Solutions for Healthcare Data Migration

Having worked with numerous healthcare organizations, we’ve encountered a range of challenges during the HL7 to FHIR migration. But with our expertise, we know exactly how to navigate and solve these issues to ensure a smooth transition. Here’s how we handle some of the most common challenges:

Challenge 1: Data Mapping Complexity

HL7 (v2/v3) and FHIR have fundamentally different data structures. HL7 uses a segment-based format (e.g., PID, PV1), while FHIR is resource-based (e.g., Patient, Encounter). This makes converting thousands of HL7 messages into FHIR resources both time-consuming and error-prone.

Solution:

• Use Automated Mapping Tools: We leverage tools like Microsoft FHIR Converter, HAPI FHIR, and IBM FHIR Server to auto-map HL7 segments to FHIR resources. Custom FHIR profiles are used to enforce organization-specific rules.
• Engage FHIR Experts: We partner with healthcare interoperability specialists (like our team) to optimize mapping logic and ensure seamless conversion.
• Adopt Incremental Migration: We start by migrating high-impact data such as Patient and Lab Results before addressing more complex workflows, ensuring minimal disruption.

Challenge 2: Data Integrity and Loss

Data corruption can occur if mappings are done incorrectly, especially when fields in FHIR don’t have direct equivalents in HL7 (such as custom Z-segments). This can result in incomplete records and missing critical information.

Solution:

• Implement Rigorous Validation: We use FHIR Validator and Inferno to ensure data consistency post-migration. Parallel testing helps us compare HL7 and FHIR system outputs to catch any discrepancies.
• Build a Rollback Strategy: To minimize risk, we maintain backup HL7 interfaces during the transition, allowing us to recover quickly in case of critical failures.
• Log and Monitor: Real-time monitoring tools like Splunk or ELK Stack track data discrepancies, helping us spot issues early and take corrective action swiftly.

Challenge 3: Resistance to Change

Clinicians and IT teams accustomed to HL7 workflows may resist adopting FHIR, and a lack of training can lead to poor adoption and inefficiencies.

Solution:

• Stakeholder Education: We host workshops to demonstrate FHIR’s benefits, including faster access to patient data and better app integrations (e.g., telehealth and AI tools). We also share success stories, such as hospitals that cut report delays by 50% with FHIR.
• Involve End Users Early: We pilot FHIR with a small team or department to gather feedback and fine-tune the implementation before a full organization-wide rollout.
• Gamify Training: We use interactive sandboxes, like the SMART on FHIR playground, to let clinicians and IT teams experiment with FHIR risk-free, encouraging adoption and hands-on learning.

Tools and APIs for Migrating Healthcare Data

When we help our clients migrate healthcare data from HL7 to FHIR, we rely on a set of proven tools, APIs, and frameworks that ensure a smooth, efficient, and compliant transition. These tools make the migration process easier, secure, and scalable, allowing us to integrate healthcare systems seamlessly and maintain data integrity. Here are the tools we use:

1. FHIR Conversion Tools

HAPI FHIR

We use HAPI FHIR, a robust open-source library for Java, to manage and convert FHIR resources. It simplifies the process of converting HL7 data into FHIR-compatible formats, making integration with existing systems much easier. HAPI FHIR allows us to streamline the migration process, saving time while ensuring accurate data transformation.

Redox FHIR Connector

Redox’s FHIR Connector is a key tool for connecting legacy healthcare systems to FHIR-based applications. It enables seamless data exchange between different platforms, ensuring that your healthcare data flows securely and efficiently. We use this tool to ensure that our clients’ systems are FHIR-ready without compromising on interoperability.

2. APIs for Data Integration

SMART on FHIR

We integrate SMART on FHIR to provide secure access to patient data using OAuth2 protocols. This API allows us to build applications that easily connect to EHRs in real time. It’s a powerful tool for ensuring secure, compliant, and seamless data exchange across healthcare applications.

FHIR API by Google Cloud Healthcare

For clients moving to the cloud, we leverage the FHIR API by Google Cloud Healthcare. This API allows us to store, manage, and access patient data in a secure and scalable cloud environment. It simplifies the process of implementing FHIR and ensures that cloud solutions remain compliant with healthcare regulations.

3. Middleware and Integration Platforms

MuleSoft

MuleSoft’s Anypoint Platform is one of our favorite integration tools for healthcare data migration. It provides pre-built connectors and an API-led connectivity approach, making it easier to link various healthcare systems using HL7 and FHIR standards. MuleSoft helps us streamline integrations and ensure that data flows securely across platforms.

Rhapsody Integration Engine

Rhapsody Integration Engine is another platform we often use to bridge the gap between legacy HL7 systems and modern FHIR platforms. This comprehensive integration engine ensures that data is exchanged smoothly, without friction, helping our clients transition seamlessly while maintaining the security and accuracy of their healthcare data.

4. FHIR Validation and Testing Tools

FHIR Validator

Before finalizing the migration, we always run data through the FHIR Validator. This tool checks that the data is correctly formatted and compliant with FHIR standards, ensuring that everything is in place for successful integration. It’s an essential tool for verifying data integrity and catching errors early in the migration process.

Firely FHIR Tools

Firely FHIR Tools are invaluable for testing and validating FHIR data. These tools help us ensure that the data we migrate from HL7 to FHIR is both accurate and compliant. Firely’s validation suite makes it easy to identify issues during testing, ensuring that the final FHIR implementation is reliable and high-quality.

Case Study: HL7 to FHIR Migration in a Large EHR Platform

One of our clients, a leading enterprise healthcare platform managing patient records across over 200 hospitals and clinics, faced significant interoperability challenges with its legacy HL7-based EHR system. The existing system was unable to keep up with the growing demand for data integration and real-time communication, hindering their ability to offer timely and coordinated care. Here’s how we worked with them to transition from HL7 to FHIR and achieve a future-ready platform.

Key Pain Points:

• Inconsistent Patient Data: Variations in HL7 message formats across different hospitals and clinics led to inconsistent and unreliable patient data.
• Slow and Costly Integrations: Integrating with third-party applications, such as telehealth platforms, analytics systems, and wearables, was slow and expensive due to the reliance on custom HL7 interfaces.
• Regulatory Pressure: With the ONC’s push for FHIR adoption by 2025, the organization faced increasing pressure to comply with new data exchange mandates.

The client decided to migrate to FHIR to address these challenges and to:

• Enable real-time data sharing with external partners such as labs, pharmacies, and telehealth platforms.
• Reduce integration costs and complexity by streamlining data exchanges.
• Improve clinician and patient experience by enabling faster access to accurate patient data.

Solution

Mapping Data to FHIR Resources

The first step was to map the existing HL7 data, such as patient information, observations, and encounters, into FHIR’s standardized resources. Using tools like Microsoft FHIR Converter, we automated the mapping process, ensuring consistency and accuracy in the migration of data.

SMART on FHIR for External Application Integration

To address the integration complexity, we implemented SMART on FHIR, a widely adopted API framework. This allowed for seamless, secure data exchange between the upgraded EHR system and external healthcare applications. By leveraging SMART on FHIR, the platform could integrate with third-party apps more efficiently, including telehealth services, analytics platforms, and wearables, without custom interfaces.

Results

Regulatory Compliance Achieved

The client successfully met ONC’s 2025 interoperability rules ahead of schedule, establishing themselves as a leader in FHIR adoption among EHR vendors.

Lessons Learned

• Start small: Piloting migrations with one facility reduces risk and allows for testing and fine-tuning before scaling.
• Automate mappings: Tools like HAPI FHIR ensure that data is mapped correctly, preventing errors and reducing manual effort.
• Train early: Clinician and IT team buy-in is critical for successful adoption. Starting training early helps ensure smooth transitions.

Conclusion

Migrating from HL7 to FHIR is crucial for modernizing healthcare platforms and ensuring seamless data interoperability. As the healthcare industry continues its digital transformation, FHIR will play a key role in enabling real-time data exchange, improving patient care, and supporting innovative solutions. At Ideausher, we specialize in helping organizations navigate the complexities of HL7 to FHIR migration, offering expert support to ensure a smooth and efficient integration process.

Looking to Migrate Healthcare Data from HL7 to FHIR?

Upgrade your healthcare data systems to FHIR for seamless interoperability, real-time data exchange, and future-proof compliance. At Idea Usher, we make your migration from HL7 to FHIR smooth, secure, and scalable, so you can focus on delivering better patient care without the hassle of complex technical challenges. Let us handle the migration while you continue to enhance the patient experience.

Why Choose Us?

• 500,000+ hours of coding expertise – Our developers, with experience at top tech companies, ensure flawless execution.
• End-to-end migration – We handle everything from HL7 mapping to FHIR deployment, guiding you every step of the way.
• Compliance-ready – We make sure your system aligns with HIPAA, USCDI, and CMS regulations, effortlessly.

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