How to Handle FHIR Version Mismatches Across Hospital Systems (R4, STU3, R5)

Anatolii Ivaniuk /

7 August 2025

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Development Outsourcing

FHIR version mismatches are a common challenge for hospitals using different FHIR standards like STU3, R4, and R5. These mismatches disrupt workflows, compromise data accuracy, and create integration issues. Here's how to address them effectively:

• Understand the Versions:
  • STU3: Trial use, limited regulatory support, declining adoption.
  • R4: Normative, widely used, strong regulatory backing.
  • R5: Trial use, improved features but early adoption stage.
• Key Challenges:
  • Field changes and resource differences between versions.
  • Missing or removed resources causing compatibility gaps.
  • Workflow disruptions due to inconsistent data handling.
• Solutions:
  • Proxy Layers: Translate data between versions, ensure compatibility, and enhance security.
  • Tools: Use platforms like HAPI FHIR, Firely Server, or cloud services (Azure, Google, AWS) to manage multiple FHIR versions.
  • Testing: Validate systems with tools like Touchstone and Inferno to ensure smooth transitions.
• Plan for Upgrades:
  • Use proxy layers during transitions.
  • Maintain flexible APIs that support multiple versions.
  • Document changes, train teams, and follow regulatory guidelines.

Quick Comparison of FHIR Versions:

Getting To Know FHIR - The Best Explanation of FHIR They've Ever Heard

FHIR Versions Currently Used in Hospitals

In the U.S., hospitals predominantly rely on three FHIR versions - STU3, R4, and R5. Each version serves a specific purpose and comes with its own set of strengths and challenges. These differences contribute to the integration hurdles many healthcare systems face, as explored later in this guide.

Main Features of STU3, R4, and R5

FHIR STU3 introduced expanded data models and workflows but was primarily intended for trial use. Its experimental nature made it less suited for critical, high-stakes healthcare systems.

FHIR R4 marked a turning point as the first normative version. With finalized core resources that remain unchanged in future updates, it provided the stability hospitals needed. This version also gained strong regulatory support, particularly under mandates like the Cures Act, leading to widespread adoption across electronic health record (EHR) systems.

FHIR R5, the latest iteration, builds on R4 by offering improved data exchange capabilities, enhanced workflow automation, and broader standardization. It introduces additional resources, stronger security measures, and better support for real-time data exchange. For those seeking a middle ground, FHIR R4B combines the stability of R4 with selected features from R5.

These varying features and levels of stability influence how hospitals approach clinical data exchange, with R4 emerging as a reliable standard for most systems.

Usage Patterns and Regulatory Requirements

Regulatory mandates play a significant role in shaping FHIR adoption. FHIR R4 is currently the most widely used version worldwide, serving as the primary standard in 31 countries. Its regulatory backing, particularly for patient data access, has cemented its dominance.

By 2025, 71% of respondents anticipate FHIR being used in their country for at least "a few use cases", while 73% of countries with electronic health data exchange regulations either mandate or recommend FHIR. Although R4 remains the frontrunner, newer versions like R4B and R5 are gradually gaining attention, even though their adoption is still in early stages. Hospitals must carefully balance the need for innovation with the reliability of established standards.

Upgrading to newer FHIR versions isn't always straightforward. Legacy systems often require extensive training and customization to transition from older standards. Unlike traditional standards like HL7 V2/V3 and CDA, which rely on batch processing, FHIR enables real-time data sharing, offering a modernized approach to interoperability.

FHIR Version Comparison Chart

This comparison highlights why R4 has become the preferred choice for hospitals. Its stability, coupled with strong regulatory backing, positions it as the go-to standard, even as newer versions begin to emerge. Looking ahead, 54% of respondents expect FHIR adoption to grow significantly in the coming years.

The coexistence of multiple FHIR versions often leads to compatibility challenges. For instance, a cardiology department operating on R4 might struggle to exchange data with a lab system still using STU3. These challenges underline the importance of technical solutions, such as proxy layers, which are discussed in the sections that follow.

Problems Caused by FHIR Version Mismatches

When hospital systems rely on different FHIR versions, the resulting mismatches can disrupt operations, compromise data accuracy, and put patient care at risk. These technical inconsistencies can skew data interpretation and create significant integration challenges.

Field Changes and Resource Differences

One major issue stems from changes in data structures between FHIR versions. Fields that exist in one version may be renamed, reformatted, or reorganized in another. This can lead to data being misinterpreted or even lost during exchanges. For example, validation tests have shown challenges in converting data types like fhir:code and fhir:anyURI across schema formats. These differences often result in failures during data processing.

Changes to resource structures add another layer of complexity. Critical elements, such as medication dosages, may not align properly between systems. This misalignment can lead to the loss or misinterpretation of essential clinical details, further complicating data sharing.

Missing or Removed Resources

Problems escalate when newer FHIR versions introduce resources that older systems cannot recognize. This creates a compatibility gap, where modern systems produce data that legacy systems are unable to process. For instance, while STU3 supported 109 resources as of September 2016, later versions expanded the resource set significantly.

Imagine a scenario where one department upgrades to R5, but the pharmacy system remains on STU3. In such cases, entire categories of clinical data might become inaccessible. Validation tests have highlighted issues where resource references often include untyped entries, and URLs fail to specify reference types. These problems prevent older systems from processing incoming data, introducing further complications to clinical workflows. Even minor conversion errors can disrupt critical patient transfers.

Workflow Disruptions from Version Conflicts

The combined effects of data mismatches and missing resources can disrupt entire clinical workflows. For example, during urgent patient transfers, conversion errors might require manual intervention, delaying critical decisions.

Inconsistent coding within required CodeableConcept fields can also lead to misinterpretations of patient data. Without careful planning and robust technical solutions, such disruptions can directly affect patient outcomes and undermine system reliability. The need for efficient FHIR version management is clear, as even small discrepancies can ripple across workflows and impact care delivery.

Setting Up a Proxy Layer for FHIR Version Management

Using a proxy layer can help tackle the version mismatch challenges between different FHIR systems. Acting as a middleman, it translates data formats, bridges compatibility issues, and ensures seamless communication across varying FHIR environments.

How Proxy Layers Work

A proxy layer operates between healthcare applications and FHIR servers, managing data exchanges. Darren Devitt puts it simply:

"For consumers, the Intercept Layer IS the FHIR API".

This setup allows the proxy to manage complex version translations behind the scenes. It adjusts requests and responses in real time, converting data structures between FHIR versions. For example, if a system using FHIR R4 needs to interact with one running STU3, the proxy translates field names, restructures resources, and ensures compatibility.

Beyond translation, the proxy performs business validations, assigns version IDs, logs audit events for compliance, and blocks access to unsupported resources that could cause errors. It also enforces conditional requests and modifies payloads to maintain data integrity.

API Gateways take these capabilities further by centralizing API management, safeguarding public FHIR APIs from threats, and allowing for custom logic. Features like intelligent routing, request composition, and advanced audit and security measures enhance their functionality. Proxy servers can even modify FHIR server responses to include the proxy address, effectively masking the original server URL from client applications. These capabilities not only improve communication but also bolster security.

Benefits of Proxy Layers

Proxies don't just handle version translation - they simplify API management, improve security, and provide operational flexibility.

• Centralized Management: Proxies provide a stable interface for client applications, meaning backend systems can be updated or replaced without impacting connected apps.
• Enhanced Security: By integrating with Identity and Access Management (IAM) systems, proxies streamline authentication, enforce role-based access, and implement safeguards like rate limiting to prevent abuse such as DDoS attacks.
• Operational Flexibility: Proxies can inspect, route, or block requests based on specific rules. This allows older FHIR servers to support advanced operations indirectly. Hospitals can also implement custom workflows, IP-based access controls, and complex authorization setups.

Implementation Guidelines

To fully utilize a proxy layer, it should serve as the unified entry point for all applications while adhering to US healthcare regulations. Intelligent routing is essential to direct requests to the right backend services and balance workloads.

Authentication and authorization are critical for HIPAA compliance. The proxy should integrate with existing IAM systems and support OAuth2 protocols. In Microsoft environments, configuring the SMART on FHIR proxy with proper authentication settings and reply URLs is key.

Security measures should include Web Application Firewall (WAF) integration, IP-based access controls, and comprehensive audit logging. Detailed audit logs are essential for tracking data access and modifications, supporting both compliance and security monitoring.

While proxies offer many advantages, they come with trade-offs. They add complexity to system architecture, can introduce performance overhead due to additional processing, and may complicate debugging efforts.

Carefully assess your system's architecture, goals, and team capabilities before committing to a proxy solution. With nearly 98% of U.S. hospitals now offering FHIR-enabled APIs, as noted in the 2024 State of FHIR study, implementing a proxy layer is increasingly important for maintaining interoperability in modern healthcare systems.

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Planning FHIR Version Upgrades

Upgrading FHIR versions requires careful planning to avoid disruptions in care delivery. These upgrades often introduce backward compatibility challenges across EHRs, APIs, and applications. To navigate these complexities, hospitals need structured strategies that minimize risks while ensuring system reliability and performance. Below are key approaches to managing proxy layers, API design, and change management during upgrades.

Installing or Removing Proxy Layers

Proxy layers can play a crucial role during version upgrades by acting as a buffer for legacy systems while backend updates are implemented. These layers are particularly useful during transitional periods. Start by evaluating your existing FHIR setup to identify dependencies on older versions. Determine which resources, extensions, and APIs need updates, and decide whether to add or remove proxy layers based on this assessment.

For instance, when upgrading from STU3 to R4, proxy layers can help translate data structures while backend systems are being modernized. Tools designed for FHIR version mapping can automate the process of converting older formats into R4 or R5-compatible structures. If removing proxy layers, consider a phased migration approach, transitioning specific modules incrementally to reduce risks.

Maintaining Clean and Flexible APIs

Well-designed APIs are the backbone of smooth operations and future upgrades. Middleware can bridge compatibility gaps between older and newer FHIR versions, ensuring API stability even as backend systems evolve. To enhance flexibility, design APIs with multiple endpoints to support different FHIR versions simultaneously. This allows systems to connect using their native FHIR versions while translations occur in the background.

Investing in infrastructure that supports multiple FHIR versions is equally important. Maintain up-to-date, version-specific API documentation to ensure clarity and consistency. Once your APIs are stable, thorough documentation and robust change management practices will help safeguard the upgrade process.

Documentation and Change Management

Strong documentation and governance are critical during FHIR upgrades. Conduct detailed conformance testing and document the results comprehensively. It's also essential to train developers and clinical teams on the nuances of the new FHIR version, including workflow changes and troubleshooting techniques.

Establish clear change management protocols, complete with rollback plans and a thorough understanding of system dependencies. Aligning with standards from organizations like ONC, HL7, and CMS can further refine your upgrade strategy.

Engage with FHIR experts and vendors to mitigate risks and streamline the migration process. Participation in the FHIR community is also valuable - HL7 releases new FHIR versions every 18 to 24 months and provides guidance on stability levels (Normative, Trial Use, Draft, Informative, and Deprecated), helping you determine the right time to adopt new features.

Finally, remember that FHIR fragmentation is an ongoing challenge. Even after completing an upgrade, you’ll likely need to manage multiple FHIR versions to accommodate varying implementations across hospitals and vendors. Your planning should account for this ongoing version management to ensure long-term success.

Tools and Testing for FHIR Version Management

Effectively managing FHIR version mismatches requires a thoughtful approach, combining the right tools and thorough testing methods. The healthcare industry has developed a range of solutions to tackle version fragmentation, from testing platforms to servers capable of supporting multiple FHIR versions simultaneously. By integrating these tools with strategies like proxy layers and API upgrades, you can ensure smoother version management.

Common FHIR Version Management Tools

HAPI FHIR is a powerful open-source tool that supports FHIR versions DSTU2, STU3, R4, and R5, making it well-suited for legacy hospital systems. Built on Java, it features a RESTful interface and offers robust mapping capabilities between FHIR versions. It also supports FHIR R4B, which integrates some R5 features into R4. However, developers should be aware of potential validator limitations when working with R4B. HAPI FHIR complements proxy layers by ensuring seamless version translations.

Firely Server enables multiple FHIR versions - STU3, R4, and R5 - to run side-by-side on a single server instance. Since version 3.0.0, developers can specify the desired version using the fhirVersion parameter in the Accept or Content-Type header. For example, to search for all Patients in STU3, a GET request might look like this:

GET <base>/Patient Accept: application/fhir+json; fhirVersion=3.0 

Cloud-based solutions also provide flexibility. Azure Health Data Services supports STU3 and R4 using .NET and C#. The Google Cloud Healthcare API handles DSTU2, STU3, and R4 across languages like Go, Java, Node.js, and Python. Meanwhile, AWS HealthLake offers support for STU3 and R4 through its FHIR APIs.

For SQL-based querying, FHIRbase supports R4 and DSTU3, while the Aidbox FHIR Platform offers cloud-based R4 support with REST, GraphQL, and SQL query options.

Testing Setup and Methods

Building on strategies like proxy layers and API management, rigorous testing is crucial for ensuring smooth FHIR version transitions. Testing environments validate compatibility before deploying changes to production systems. Tools like Touchstone and Inferno are widely used for verifying conformance with FHIR specifications and ONC certification criteria.

Touchstone provides a highly adaptable testing framework, ideal for organizations with diverse needs. Users can register, define their Test System, and run automated interoperability tests.

Inferno, on the other hand, offers a simpler setup with fewer adjustments, making it quicker to implement. Its process involves registering on the platform, defining the Test System with system details and supported formats, and running automated tests to evaluate both FHIR server and client implementations.

For handling version-specific differences, TestScript resources allow for dynamic operations. Advanced testing scenarios can also benefit from cross-version compatibility techniques. For instance, the FHIR Terminology Ecosystem IG shows how R5 test cases can be adapted for R4 servers by dynamically converting requests and responses, offering a practical model for managing version transitions.

Tool Feature Comparison

When choosing tools, focus on more than just FHIR version support. Consider factors like licensing, deployment options (on-premise, cloud, or hybrid), programming language compatibility, and global availability.

The decision between Touchstone and Inferno depends on your testing needs. Touchstone is better for organizations requiring extensive customization, while Inferno is ideal for teams looking for a straightforward, quick-to-implement solution.

Keep in mind that FHIR versions are updated approximately every 18–24 months, with newer releases potentially deprecating or removing features from older versions. Your choice of tools should account for this ongoing evolution and provide the flexibility needed for future migrations.

Conclusion: Preparing for Future FHIR Versions

Addressing FHIR version mismatches isn't just about resolving today's issues - it's also about getting ready for what's next. With FHIR R6 expected to enter its first normative ballot in 2026, healthcare organizations must focus on strategies that meet immediate needs while staying adaptable for future changes.

To prepare, start by evaluating your current FHIR implementations. Pinpoint any legacy dependencies and consider phased migration plans. Using proxy and middleware solutions can help avoid disruptions during this process. Incorporating AI and automation into your approach can also streamline transitions. These tools can handle tasks like automated version mapping, compatibility checks, dynamic data conversion, and governance monitoring far more efficiently than manual methods.

Supporting multiple FHIR versions simultaneously is another smart move. This allows you to maintain compatibility while transitioning to newer standards. Alongside this, ensure your teams are well-trained on emerging standards and work closely with FHIR experts to reduce risks during implementation.

It's worth noting that FHIR R4 remains the most widely adopted version, while R5 introduces some valuable updates but is still primarily in trial use. Balancing the need for current compatibility with the push toward future standards is key to maintaining smooth operations and interoperability.

Finally, design your systems with versioning in mind from the very beginning. This forward-thinking approach will help you stay competitive and compliant as FHIR continues to evolve.

FAQs

How can proxy layers resolve FHIR version mismatches in hospital systems?

Proxy layers serve as a crucial link between various FHIR versions like R4, STU3, and R5, enabling smooth data exchange across hospital systems. They handle tasks like translating data formats, adapting to field changes, and compensating for missing resources. This ensures systems remain interoperable and avoids potential integration headaches.

With proxy layers in place, hospitals can update or adjust their FHIR implementations without interrupting current workflows or APIs. This makes managing different versions more straightforward, allowing systems to communicate reliably while staying adaptable for future needs.

What challenges do hospitals face when upgrading from older FHIR versions like STU3 to newer ones such as R4 or R5?

Upgrading from older FHIR versions like STU3 to newer ones such as R4 or R5 can be a tricky process for hospitals. The challenges often revolve around handling breaking changes in FHIR standards, ensuring system compatibility when different versions are in play, and reshaping existing data models to fit the updated specifications.

Hospitals may face hurdles such as missing or modified resources, integrating new FHIR elements into older systems, and preserving interoperability throughout the upgrade. Successfully navigating these transitions requires a well-thought-out plan, extensive testing, and tools like FHIR proxies or custom mappers to bridge the gaps between versions. With a strategic approach, hospitals can manage these upgrades without interrupting clinical workflows.

Why is FHIR R4 the most commonly used version in hospitals, and how does it differ from STU3 and R5?

FHIR R4 has become the go-to version for hospitals because it's the first normative release. This means its core elements are stable and dependable for long-term use - qualities that healthcare providers value when implementing standardized data exchange systems.

By comparison, STU3 is an earlier iteration developed during the standard's initial phases, which makes it less stable. Meanwhile, R5 introduces advanced features but hasn’t yet seen widespread adoption, as it’s primarily used for experimental or cutting-edge projects. Hospitals tend to stick with R4 due to its maturity and reliability, ensuring it meets critical interoperability requirements without the uncertainties tied to newer or earlier versions.

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