During the twenty-first century, the development of national immunization programmes (NIP) has matured into robust processes where evidence-based methodologies and frameworks have increasingly been adopted. A key role in the decision-making and recommending processes is played by National Immunization Technical Advisory Groups (NITAGs). In a survey performed among European Union member states, Norway and Iceland, in February 2013, 85% of the 27 responding countries reported having established a NITAG, and of these, 45% have formal frameworks in place for the systematic development of vaccination recommendations. Independent of whether a formal framework is in place, common key factors are addressed by all NITAGs and also in countries without NITAGs. The four main factors addressed by all were: disease burden in the country, severity of the disease, vaccine effectiveness or efficacy, and vaccine safety at population level. Mathematical modelling and cost-effectiveness analyses are still not common tools. Differences in the relative weighting of these key factors, differences in data or assumptions on country-specific key factors, and differences in existing vaccination systems and financing, are likely to be reasons for differences in NITAG recommendations, and eventually NIPs, across Europe. Even if harmonization of NIPs is presently not a reasonable aim, systematic reviews and the development of mathematical/economic models could be performed at supranational level, thus sharing resources and easing the present work-load of NITAGs. Nevertheless, it has been argued that harmonization would ease central purchase of vaccines, thus reducing the price and increasing access to new vaccines.