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Background: This paper crystallises the experience developed by the pan-European PALANTE Consortium in dealing with the generation of relevant evidence from heterogeneous eHealth services for patient empowerment in nine European Regions. The European Commission (EC) recently funded a number of pan-European eHealth projects aimed at empowering European patients/citizens thus transforming the traditional patient/citizen role in the management of their health (e.g., PALANTE, SUSTAIN, CARRE, HeartCycle, Empower). However, the heterogeneity of the healthcare systems, of the implemented services and of the target patients, the use of ad-hoc definitions of the salient concepts and the development of small-size experiences have prevented the dissemination of "global" results and the development of cumulative knowledge. The main challenge has been the generation of large-scale evidence from heterogeneous small-size experiences. Discussion: Three lessons have been collectively learnt during the development of the PALANTE project, which involves 9 sites that have implemented different eHealth services for empowering different typologies of patients. These lessons have been refined progressively through project meetings, reviews with the EC Project Officer and Reviewers. The paper illustrates the ten steps followed to develop the three lessons. The first lesson learnt is about how EC-funded projects should develop cumulative knowledge by avoiding self-crafted measures of outcome and by adopting literature-grounded definitions and scales. The second lesson learnt is about how EC-funded projects should identify ambitious, cross-pilot policy and research questions that allow pooling of data from across heterogeneous experiences even if a multi-centre study design was not agreed before. The third lesson learnt is about how EC-funded projects should open their collections of data and make them freely-accessible to the scientific community shortly after the conclusion of the project in order to guarantee the replicability of results and conclusions. Summary: The three lessons might provide original elements for fuelling the ongoing debate about the capability of the EC to develop evidence-based policies by pooling evidence from heterogeneous, local experiences. [ABSTRACT FROM AUTHOR]