We use entropy statistics in this paper to measure the synergies of knowledge exploration, knowledge exploitation, and organizational control in the Hungarian innovation system. Our data consists of high-tech, medium-tech firms, and knowledge-intensive services categorized in terms of sub-regions (proxy for geography), industrial sectors (proxy for technology), and firm size (proxy for organization). Configurational information among these three dimensions is used as an indicator of the reduction of uncertainty or, in other words, the synergy among the knowledge functions. The results indicate that three regimes were generated in the Hungarian transition period with very different dynamics: (1) Budapest and its agglomeration emerge as a knowledge-based innovation system on every indicator; (2) in the north-western part of the country, foreign-owned companies and FDI have induced a shift in knowledgeorganization; while (3) the system seems to be organized in the eastern and southern part of the country in accordance with government expenditures. The national level no longer adds to the synergy among these regional innovation systems.