The purpose of this study is to investigate empirically the role of innovation activity in 16+1 cooperation, within the Central and Eastern Europe (CEE). We also identified those internal and external factors, which might cause improvements in innovation performance of CEE companies. Our main focus was on technology-based research and innovations. We applied qualitative research methods. Our findings demonstrate that CEE companies have significant contribution to performance. We found that key success factors of these organisations are based on four elements: knowledge management, access to financial resources, managing formal and informal networks, as well as achieving synergies between technological and non-technological innovations. The preparation of the analytical study was facilitated by being part of a Slovenian-Hungarian MASH European Grouping of Territorial Cooperation and thus, through our cross-border relations, we have more information, we are deeper into the functioning and / or non-functioning EU systems.