Immunisation schedules are developed by national committees on immunisation and may differ considerably between the European Union (EU) member states (MS). The European Commission has launched an initiative for a council recommendation with the aim to establish a scientifically substantiated reference childhood immunisation schedule for the EU. In our view this initiative implies the establishment of one European childhood immunisation schedule, which could lead to the perception that this schedule is the only one scientifically justified. The expectations that one uniform immunisation schedule will facilitate mobility of EU residents, improve data collection and increase vaccination coverage are either quantitatively or qualitatively not relevant or even ethically problematic. Arguments that uniform schedules would lead to lower vaccine prices and reduce the need for clinical trials appear to be more relevant but could be addressed more effectively by other measures. On the other hand the following factors may differ substantially between MS and thus support different immunisation schedules, such as (a) values and goals, (b) epidemiological situation, (c) health care delivery system, (d) logistics of vaccine delivery and (e) economic situation. We argue that uniform schedules should not be perceived as a goal in itself but rather as a possibly desired by-product following increasing agreement on goals and values between MS and improved evidence base to be used by national committees on immunisation.