Regional disparities in the European Union are evaluated from the environmental and innovation capacity point of view. A high Gross domestic product, productivity or innovations typically occur in the regions of the “old” western and northern Europe, often in the metropolitan regions and the opposite situation is can be found in the new member states. Summary Innovation Index (SII) is a composite index developed for an overview of the relative national and regional innovation performance. The leading countries as measured by SII are Finland, Sweden, Denmark and Germany and the innovation disparities explain economic trends in the EU countries. Environmental indices are also rather complex although a positive correlation can be shown with the innovation indicators. The Ecological Footprint as compared with the Environmental Sustainability Index and the number of environmental patents are used to show the leadership of countries known for their positive attitude to environment, such as Scandinavian countries, Germany, Austria, France and Benelux, although the regional disparities do not follow the innovation territorial pattern