IIR is linked with the Czech Ministry of Foreign Affairs, conducting research and analytical activities concerning international relations and Czech foreign and security policies. IIR organizes conferences, seminars, and roundtable discussions of experts, academics, and political professionals on international relations, security, and development issues, linking academia and the political establishment. Striving to foster better communication between the academic community and the government and assisting in the formulation of recommendations for Czech foreign policy, IIR publishes periodical journals, specialized publications, handbooks, and study papers. IIR undertakes joint work with governmental institutions as well as with academic circles both at home and abroad, cooperating closely with a number of foreign institutions on projects ranging from international relations policy formulations to security and development analyses. IIR researchers are regularly invited to public discussion forums as experts on current issues, often visiting international conferences, and publish their work in foreign journals. IIR's library provides both students and the public with an extensive collection of foreign publications and documentation to support individual research activities.

IES offers university-level education (bachelor's, master's, and doctoral degrees in economics and finance) and functions as a research center. IES continues the prewar tradition of research and education in economics at Charles University, with an emphasis on the profound theoretical preparation of students in modern analytical methods and advanced business thinking.

CERGE-EI is a joint workplace in the field of economics, associated with two institutions: Charles University in Prague and the Academy of Sciences of the Czech Republic. CERGE itself was founded in 1991 as a US-style Ph.D. program in economics taught entirely in English. In 1992, the Economics Institut (EI) of the Academy of Sciences was created as an economics research institution to undertake substantive topical research. Recognizing their overlapping goals and interests, the two institutions entered into a cooperation agreement that later evolved into a formal joint workplace agreement. This partnership serves as a model of how to break down the artificial divisions between universities and research institutions that existed throughout the Communist period. CERGE-EI reinforces the relationship between teaching and research by creating an environment of intellectual curiosity and scientific rigor.

CDFE was originally established to serve as the Czechoslovak Representative Office of the Central Europe Institute in Washington, DC. Eighteen months later, the center was transformed into a private, nonpartisan, nonprofit Czech foundation charged with conducting and organizing educational exchanges, internships, training in democratic institutions and research in market economics. The main goal of CDFE is the promotion of democratic thinking and active citizen participation in the democratic process. A secondary goal is to provide information about NATO and the EU, and to aid the integration of the Czech Republic into these structures.