This paper investigates on the presence of innovation clusters in the European regions. The analysis is based on a databank set up by CRENoS on regional patenting at the European Patent Office classified by ISIC sectors (2 digit), which considers 175 regions of 17 countries in Europe. Firstly, an analysis of the spatial distribution of innovation activities in Europe is performed. Some global and local indicators for spatial association are presented, indicating the presence of a general dependence process in the distribution of the phenomena under examination. The analysis is implemented for 23 manufacturing sectors to assess for the presence of significant differences in their spatial features. Moreover, the extent and strength of spatial externalities are evaluated for two periods: 1994-96 and 1999-01. Secondly, this paper contributes to the analysis of the process of spatial agglomeration of innovative activities by investigating directly its determinants. Our main purpose is to identify the extent to which the degree of specialisation or diversity in a region may affect the innovative activities in a particular local industry. Other local factors are also tested such as home market effect and other agglomeration phenomena. Moreover the geographical extent of such effects is measured by means of the usual tests of spatial econometrics.