RD-Connect is an infrastructure for rare disease research bringing together multiple data types in three systems: Genome-Phenome Analysis Platform (platform.rd-connect.eu), Sample Catalogue (samples.rd-connect.eu) and Registry & Biobank Finder (catalogue.rd-connect.eu). All these systems are open to any rare disease and available free of charge. The Genome-Phenome Analysis Platform is a centralized data repository and a user-friendly online analysis system combining omics data (genomics, proteomics, transcriptomics) with clinical information at individual-patient, family or cohort level. Whole-genome, exome and gene panel datasets are submitted by the end-user and processed by RD-Connect's standardised analysis and annotation pipeline to make data from different sequencing providers comparable. Raw data is deposited at the European Genome-phenome Archive (EGA) for long-term storage. Clinical information is recorded in the PhenoTips system, which simplifies entry of clinical data using the Human Phenotype Ontology. Results are available to the submitter and authorised users through the highly configurable platform, which enables advanced filtering and prioritization of variants. Users can analyse their own patients and compare results with other submitted cohorts, including queries such as: “Does this variant exist in this cohort?” and “Are there patients in other databases with matching phenotype and candidate variant in the same gene?”. The Platform already includes thousands of datasets from partner projects such as NeurOmics (www.rd-neuromics.eu) and BBMRI-LPC (www.bbmri-lpc.org). In 2018, it became the primary data sharing and analysis platform for the new Solve-RD project, which will bring in 19,000 unsolved cases from European Reference Networks over 5 years. RD-Connect is free and open for contributions from individual research groups and other projects: contact platform@rd-connect.eu. The Sample Catalogue allows browsing biosample collections stored in rare disease biobanks using powerful filtering functions. It provides detailed information about individual biosamples, including disease, diagnosis type, sample type, sex, availability of genetic and registry data and of samples from the patient’s relatives. Currently, the Sample Catalogue includes over 25,000 samples stored by rare disease biobanks in the EuroBioBank Network. The work is ongoing to make the Sample Catalogue interconnected with the Platform, to enable finding biosamples from patients with a specific genetic variant, and with the Registry & Biobank Finder, to allow direct link from the global directory of rare disease databases to the sample collections.