Rare disease information is scarce within a given national context with national databases containing small number of data. At the same time providing access to much higher amount of data distributed among different national databases could provide much needed information for medical practitioners. Such an access requires the integration of these databases and assuring the privacy and data protection of the patients. This paper presents practical issues and challenges that have appeared while integrating Polish national database POLVAS into the European network within the framework of the FAIRVASC European project.