Rare lung diseases affect 1.5–3 million people in Europe while causing bad prognosis or early deaths for patients. The European Reference Network for Respiratory Diseases (ERN-Lung) is a patient centric network, funded by the European Union (EU). The aims of ERN-LUNG is to increase healthcare and research regarding rare respiratory diseases. An initial need for cross-border healthcare and research is the use of registries and databases. A typical problem in registries for RDs is the data exchange, since the registries use different kind of data with different types or descriptions. Therefore, ERN-Lung decided to create a new Registry Data-Warehouse (RDW) where different existing registries are connected to enable cross-border healthcare within ERN-Lung. This work facilitates the aims, conception and implementation for the RDW, while considering a semantic interoperability approach. We created a common dataset (CDS) to have a common descriptions of respiratory diseases patients within the ERN registries. We further developed the RDW based on Open Source Registry System for Rare Diseases (OSSE), which includes a Metadata Repository with the Samply.MDR to unique describe data for the minimal dataset. Within the RDW, data from existing registries is not stored in a central database. The RDW uses the approach of the “Decentral Search” and can send requests to the connected registries, whereas only aggregated data is returned about how many patients with specific characteristics are available. However, further work is needed to connect the different existing registries to the RDW and to perform first studies.