FHIR is not a database and FHIR queries are not SQL. What’s the solution if you have large analytical requirements for your FHIR data?
The big cloud providers have all arrived at the same conclusion.
You copy your FHIR data into a data warehouse and run your heavy duty queries there. It may not be ideal, but it’s the direction everyone is moving in.
Microsoft Fabric
As of 2025, Microsoft are pushing users of their Azure FHIR servers towards syncing FHIR data with “Fabric” for analytical use cases.
Fabric comes with three tiers that your FHIR data can flow through: Bronze (raw data), Silver (enriched) and Gold (curated). Fabric is relatively new, so bear that in mind when making decisions around using it.
More about Fabric: https://learn.microsoft.com/en-us/industry/healthcare/healthcare-data-solutions/overview
GCP BigQuery
Google recommends exporting your FHIR data to their Big Query data warehouse and performing your analytics there. They provide three steps:
– Perform a single export: https://cloud.google.com/healthcare-api/docs/how-tos/fhir-export-bigquery
– Stream FHIR resource changes: https://cloud.google.com/healthcare-api/docs/how-tos/fhir-bigquery-streaming
– Analyze your data: https://cloud.google.com/architecture/analyzing-fhir-data-in-bigquery
AWS Redshift
Amazon recommend using their Redshift data warehouse by way of S3 buckets. They provide a detailed blog post documenting each step of the process.
Not light reading: https://aws.amazon.com/blogs/big-data/analyzing-healthcare-fhir-data-with-amazon-redshift-partiql/
But what if you’re not on the cloud or your server provider doesn’t come with a data warehouse to migrate to?
Take a look at SQL on FHIR.
Spearheaded by Health Samurai, and with participants from Microsoft, Google and others, it takes a stab at flattening out FHIR resource data and making it accessible via SQL.
Early days but worth keeping an eye on: https://build.fhir.org/ig/FHIR/sql-on-fhir-v2/
The lesson here if you’re trying and failing to run big queries via your FHIR API is to stop and rethink.
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