Scientific excellence, and acceptance by health authorities of results derived from research on personalised medicine require standards ensuring validity and reproducibility. The objective of PERMIT is to establish, with all relevant stakeholders and invited experts, recommendations ensuring the robustness of personalised medicine trials, which also requires validation of the stratification methods. In a series of workshops participants, partners and selected experts will address the various aspects of methodology, design, data management, analysis and interpretation in personalised medicine research programmes, with the objective to reach consensus and publish recommendations. A mapping of the literature will inventory methodological practice in the various steps of personalised medicine programmes (WP2) and identify needs in terms of standardised methodology. WP3 will address the design of the stratification and validation cohorts, including the issue of the statistical power and the quality of data. WP4 will focus on the use of the stratification algorithms and the robustness the stratification methods. WP5 will address the translational step needed to select treatments to be tested in each of the clusters. WP6 will be dedicated to randomized clinical trials testing treatments in each cluster (including umbrella / basket designs), or comparing the personalised vs. non-personalised approach. Recommendations and publications in scientific journals, a final meeting and webinars will foster adoption and implementation (WP7). The PERMIT consortium is composed of participants: pan-European research infrastructures (ECRIN, EATRIS, ELIXIR-LU/UNILU), funders (DLR), HTAs (KCE, ISCIII), patients (EPF), regulatory (ISS), data protection (TMF) and scientific experts, whereas partners represent stakeholders interested in the quality of evidence generated by personalised medicine research (industry, medicine agencies, ethics committees, funders, journal editors, HTAs, BBMRI).