The recent economic crisis brought about new challenges and disrupted the previous convergence process in R&D systems of EU member countries. The new developments in the configuration of the European Research Area require the use of adequate methods for measuring disparities between EU countries and monitoring of the convergence process. In this context, our paper aims to explore the new trends in R&D disparities among different groups of EU countries by means of a specific method for assessing the convergence/divergence process, namely the “sigma convergence” indicator introduced by Barro and Sala-i-Martin (1995). Considering the sizeable heterogeneity that exists within the EU-28 and candidate countries, we performed separate analyses on two groups of countries that are likely to be more homogenous: old and new EU member countries. Our main finding is a convergence trend for both EU-28 and candidate countries and old EU members over 2006-2013, while the new EU countries seem to diverge in terms of the research and development activity as captured by the Summary Innovation Index. The existence of a systematic trend of convergence / divergence was further tested based on both Augmented Dickey – Fuller (ADF) and DF- GLS stationarity tests.