Purpose –The study aims to investigate the impact of highly skilled emigration from Greece on the innovation performance of the Greek economy. Design/methodology/approach – The study draws on a new, census-scale, database that includes all the Greek Ph.D. holders and on statistical information pooled from various secondary sources. Findings – The mass emigration of highly educated Greek scientists that was exacerbated during the ten-year recession has had detrimental effects on Greece’s innovation performance. Specifically, an increase in the number of highly skilled emigrants has a negative impact on scientific citations and on patent applications during the following year. An instrumental variable approach based on gravity model literature is employed to test the authors’ findings. The potential effects of these findings and policy suggestions are also discussed. Originality/value – The study enriches the academic and policy discussion on the science and technology– related consequences of brain drain on the origin country. This is the first study that focuses on Greece – the country which experienced the highest emigration rates within the EU during the severe ten-year economic crisis – and sheds light on the impact of skilled emigration on its innovation performance.