The landscape of genetic testing is rapidly changing. Soon, whole genome sequence analysis (3Gb-testing) will be an effective and financially viable alternative to targeted gene analysis. New technologies that allow efficient sequencing of a whole human genome in a diagnostic setting will have an enormous impact on diagnostic centres replacing many existing molecular and cytogenetic tests. Patients deserve to benefit from our vastly growing knowledge on functional genomics. 3Gb-testing is the ideal method to bring these benefits to the public. However, it is critical to avoid mistakes with respect to ethics, quality, over or mis-interpretation of data. It is essential that our society is prepared for the change once it is implemented. Hence, current gaps in our knowledge have to be identified and research has to be initiated to bridge these gaps. The 3Gb-TEST project will bring stakeholders together and ensure they are informed with respect to the desirable and undesirable developments. The clinical utility and cost effectiveness of whole genome sequencing needs to be determined as part of a robust health technology assessment process (HTA). Interpretation of sequence data in terms of clinical relevance will pose a challenge to both laboratory and clinical geneticists. Substantial investments may be required and the logistic restructuring of genetic services will need to be addressed. This project aims to prepare Europe for innovations in molecular testing. Quality assessment schemes, HTA and guidelines have to be in place. Healthcare professionals must be aware of the impending change and potential impact on practice. The Consortium will inform the healthcare community and make recommendations to the European Commission, the European Society of Human Genetics, and national organizations relevant to this field. A key output will be a validated roadmap for the implementation of diagnostic genome sequencing in Europe.