Currently, patient data is geographically dispersed, difficult to access, and often stored in siloed project-specific databases preventing large-scale data aggregation, standardisation, integration, harmonisation and advanced disease modelling. The ELIXIR Cloud and Authentication & Authorisation Infrastructure (AAI) ecosystem aims to leverage a coordinated network of ELIXIR Nodes to deliver a Global Alliance for Genomic Health (GA4GH) standards-compliant federated network and infrastructure to enable population-scale genomic and phenotypic data analysis across international boundaries. Connecting distributed datasets via common standards will allow researchers unprecedented opportunities to detect rare signals in complex datasets and lay the ground for the widespread application of advanced data analysis methods in the life sciences. The ELIXIR Cloud & AAI project will lay the groundwork to deliver the foundational capability of “federation” of identities, sensitive data access, trusted hybrid HPC/Cloud providers and sensitive data analysis services across ELIXIR Nodes by underpinning the bi-directional conversation between partners with the GA4GH standards and specifications and ELIXIR trans-national expertise. The project is also developing a framework for secure access and analysis of sensitive human data based on national federations and standardised discovery protocols. The secure authentication and authorisation process alongside guidelines and compliance processes is essential to enable the community to use this data without compromising privacy and informed consent. The ecosystem provides a repository to store bioinformatics software containers and workflows, a data registry to discover and resolve the locations of datasets, interoperable workflow and task execution services to leverage ELIXIR's federated life-science infrastructure, and a web portal for end user access.