The EU Directive (2011/24/EU) on the application of patients’ rights in cross-border healthcare came into force in April 2011 and was due to be transposed by Member States into national law by October 2013. The Directive clarifies the rights of patients to seek reimbursement for healthcare received in another Member State. The EU Directive has also considered European cooperation in healthcare and importantly the establishment of the European Reference Networks for rare and low prevalence complex diseases. In preparation for the forthcoming evaluation of the Directive after almost 10 years since adoption, the European Commission has commissioned a study to enhance the implementation of Directive. Since evaluation framework of EU policies, programmes and legislation rely on an “intervention logic” and such a logic model was not developed at the time of impact assessment accompanying the proposal for the Directive in 2008, this had to be developed as part of the current preparatory study. In addition, the development of qualitative and quantitative indicators linked to the intervention logic of the Directive was requested so that to facilitate the evaluation of the Directive. It is important to emphasise that developing an intervention logic retrospectively must draw a clear line and distinguish between how the Directive was expected to work at the outset and how in practice it did work. This baseline framework will provide the future evaluator of the Directive a tool to identify not only intended but also unintended (positive and possibly negative) effects of the Directive.