Although individually uncommon, rare diseases (RDs) collectively affect 6-8% of the population; around 30M people in the EU and 400M worldwide. RD research faces specific challenges. Since patients, clinical expertise and research communities are scarce and fragmented, data sharing between researchers is crucial. To address this, in 2012 the European Commission awarded a €12M FP7 grant to RD-Connect to create an infrastructure bringing together multiple data types used in RD research into a common resource for researchers and clinicians. In six years, RD-Connect developed an integrated platform bringing together analysis tools and different types of data needed in RD research into a common resource for clinicians and researchers worldwide. The RD-Connect platform consists of three systems: Genome-Phenome Analysis Platform, Registry & Biobank Finder and Sample Catalogue, which are open to any RD. RD-Connect is open for data submissions and already holds thousands of datasets, including linked omics and phenotypic data, biosamples and information about RD patient registries and biobanks. The secure, pseudonymised datasets in RD-Connect are linked at an individual per-patient or per-sample level. Researchers can analyse data, find similar cases and related information such as availability of biomaterials. Thanks to the work on data linkage, patient registries and biobanks receive support in making their datasets Findable, Accessible, Interoperable and Reusable (FAIR). Successful collaborations with several partner projects, including NeurOmics, EURenOmics and BBMRI-LPC, led to the discovery of over 100 novel disease genes. In addition, RD-Connect has developed a number of clinical bioinformatic tools that facilitate data analysis and interpretation and are integrated in the Platform. RD-Connect ethical and legal experts developed guidelines for researchers and optimal models for data sharing, while the engagement of patients and patient representatives at every level of the project’s work ensured patient-centred approach. Collaboration with the European Reference Networks will ensure the impact of RD-Connect on improving RD patients’ quality of life. RD-Connect is embedded in European and international efforts, including BBMRI, ELIXIR and the International Rare Disease Research Consortium (IRDiRC). The project has helped move the field forward by advancing omics research and data sharing and is thus an EU flagship project and an FP7 success story.