The report outlines an ELSI (ethical, legal, societal, policy) compliant infrastructure (WG-5) for the European Union (EU) 1+Million Genomes (1+MG) data management purposes. The paper is aimed for the signatory member state policymakers. It extends the 1+MG roadmap ‘Chapter 6. Infrastructure’ in order to achieve the goals set by the declaration “Towards access to at least 1 million sequenced genomes in the EU by 2022”. We propose to divide “Infrastructure” into five connected functionalities: data discoverability, data reception, storage & interfaces, data access management mechanisms, and processing, and analysed 16 scenarios about how member states and the EU could share the responsibility to sustain these functionalities. The initiative intends to build on and extend the existing European e-Infrastructure investments to create 1+MG infrastructure functionalities. We propose that in 2021 we start a Proof of Concept with the rare disease community to explore and find ways to fill in the existing infrastructure gaps. The goal is to eventually document the technical requirements for all the 1+MG use cases in rare disease, cancer, common/population-level diseases and COVID-19 and other emerging infectious diseases, and be able to expand infrastructure activities to broader healthcare and research contexts.