This white paper was prepared to assess the opportunities and obstacles that confront us as Europe plans to make full use of the integration of genome-based data resources with resources detailing disease-based and other human phenotypes. The report represents the consensus outcome of Think Tank discussions among 17 invited experts in Brussels on October 2011. The report addresses prospects for the development and application of genotype-phenotype resources, considering them to be very promising. Establishing clear relationships (correlations) between increasing amounts of genotypic information available from clinical studies (e.g. as provided by genome wide association studies (GWAS)), and similarly of phenotype information at the population level, is still largely impossible today. This approach advocated also assists in “stratification” – instead of rejecting so many drugs during clinical trials, it could be that many deemed to be failures today will work well for sets of patients on genotypic/ phenotypic grounds.