Romania, as a country with a low R&D level, in order to converge to the living standards of western economies, is doomed to foster private investments in applied research and experimental development. Thus, it is critical to study what are the main objectives for innovation at organizational level. This paper investigates the most important objectives for innovation in Romania and in the European Union, aiming to find out what are the main challenges innovative enterprises have to face. The general approach is focused on the analysis of the frequency with which these objectives occur, both at general and structural levels. Therefore we have extracted the most important three highly important objectives for innovation, both in Romania and EU: improving the quality of goods or services, the need to increase the range of goods or services and the entering new markets or increase the market share. All these three are positively correlated with the size (number of employees) of the organization. One of our findings underlines that there are fewer objectives in EU then in Romania, both at general and structural levels. Such a situation suggesting that the differences derive from two main sources: Romania has more needs, thus the enterprises target more goals, and there is a lack of managerial know-how that leads to non-prioritized objectives for innovation. Also, we identified an asymmetry, consisting in the fact that in EU, medium sized enterprises are more likely to act as the small ones, as opposed to the Romanian context. R&D and innovation component should be in the center of the Romanian strategy for convergence and competitiveness strengthening, treating differently the SMEs in order to foster innovation in a sustainable manner, through the encouragement of private enterprises to engage in partnerships for R&D an innovation. Also there is a critical need for governmental intervention in building facilities for the modern business infrastructures (business incubators, industrial parks, clusters, and competitive poles), creating a viable VC market for innovative projects, stimulating the creation of new SMEs and fostering internationalization of the local enterprises.