As the availability of genetic tests has grown rapidly during the last decade along with the increasing knowledge of the genetic background of rare inherited diseases, sending DNA samples to another country for analysis has become more of a routine than an exception in clinical diagnostics. Nonetheless, few studies of cross-border genetic testing of rare diseases in the European Union (EU) have been carried out, and data about the challenges and problems related to cross-border testing are lacking. The purpose of this study was to investigate the experiences of the molecular genetic laboratories and the clinical genetics units concerning the cross-border genetic testing of rare diseases in the Member States of the EU. Data were collected using web-based questionnaires and phone interviews targeted at laboratories and clinical units registered with the Orphanet database. The specific aims were to clarify the volume, quality and challenges of cross-border genetic testing. The results revealed, for example, that the variability of the required documentation creates confusion and, unexpectedly, sample dispatch was considered a major problem in cross-border testing. In addition, the differences between countries regarding the reimbursement and authorization policies of cross-border testing were significant, thus confirming the pre-existing assumption about unequal access to genetic testing in the different Member States. To facilitate and organize cross-border testing, common practices need to be created at the level of the EU, and follow-up studies are needed to monitor their effects.