This report summarizes the outcomes of developing a new R&D evaluation methodology and funding system for the Czech Republic. It was undertaken by a team from Technopolis, Technology Centre ASCR, NIFU, and InfoScience Praha under contract with the Czech Ministry of Education, Youth and Sports in 2014-15. The report reviews international practices in R&D evaluation and funding, identifies key principles for the new Czech system, and provides recommendations for next steps in implementation. It categorizes Czech research organizations based on their missions and recommends using different evaluation and funding systems tailored to organization type. The report also notes some governance challenges for the Czech R&D system and emphasizes connecting the new methodology to societal needs as articulated