The main purpose of the study is to present a new approach to comparing EU regions according to their level of innovation. For many years, different organizations have published reports related to the innovation level of EU countries and regions. Usually, taxonomic methods are used to measure development in this area. The main disadvantage of this approach is that it offers an assessment of EU innovation level based only on the mean, while the main goal of this kind of analysis should include an assessment of results compatibility obtained in different areas constituting a composite measure. For this purpose, a different procedure based on the multi-criteria taxonomic method is proposed. In this method, the innovation level of every object (in the paper, EU regions) is assessed using results obtained in every group of indicators taken into account for this purpose. This means that EU regions can be divided into groups according their level of innovation in all considered areas, not only according to their mean value of development. This is the basic advantage of this type of analysis. An added value of the considerations presented in the paper is the possibility of obtaining supplementary information about the internal structure of the innovation of socio-economic objects. It should be emphasized that such analysis is a new approach to this kind of assessment. The results are especially relevant to associations such as the European Union, in which internal cohesion is one of its strategic developmental goals.