The aim of this paper is to investigate the innovation efficiency in Central and Eastern Europe by performing an input-output approach using Data Envelopment Analysis (DEA). R&D government spending and total R&D personnel stand for inputs and patent applications and high-tech exports stand for innovation outputs. We performed a comparative analysis between Czech Republic, Hungary, Poland and Romania using a 10 year-time span (2007-2016). We demonstrated that over time the innovation efficiency has improved (both regarding technical efficiency and scale efficiency) in all the four countries under scrutiny. Moreover, our research showed that the most efficient country was Hungary which balanced properly between the efforts of supporting innovation and its benefits due to reaping its positive effects in terms of high-tech exports and patent creation.