The Copernicus Center for Interdisciplinary Studies in Kraków was officially opened on October 1, 2008 but the ideas that led to its establishment had long been cultivated in Kraków. They were first undertaken by an informal group of researchers that later became the Center for Interdisciplinary Studies (OBI, or Ośrodek Badań Interdyscyplinarnych, in Polish). The history and the ideology of OBI is presented in vol. 25 of Zagadnienia Filozoficzne w Nauce, a periodical published by OBI. Currently, OBI is affiliated with the Philosophical Faculty of the Pontifical Academy of Theology (PAT) in Kraków.

The extensive activities of OBI have engaged new researchers and covered new disciplines and research subjects. As an example one can mention OBI's cooperation with the Polish Academy of Arts and Sciences (PAU), in particular with its three commissions:  the Philosophy of Natural Sciences, the History of Science and Fides et Ratio.

Another example are the Kraków Methodological Conferences, initiated by OBI, and now organized together with the Jagiellonian University (UJ) and PAU. Eminent Polish scholars as well as distinguished guests from abroad participate in these conferences and their characteristic feature is the dialogue between philosophers and scientists. It can be seen as a continuation of a long Kraków tradition, dating back to the last decades of the 19th century, when Krakow's scientists became interested in philosophical matters (Władysław Heinrich, Tadeusz Garbowski), while their students and successors (Joachim Metallmann, Leon Chwistek, Bolesław Gawecki) continued their research in this spirit by philosophizing in the context of the sciences, both the physical and the humanistic.

A different form of this dialogue materialized within the so-called Kraków Circle, established through the initiative of Jan Łukasiewwicz and comprised of Józef Maria Bocheński, Jan Salamucha, Jan Franciszek Drewnowski and Bolesław Sobociński. The main goal of the Circle was the revamping of Christian (neoscholastic) philosophy with the means offered by modern methodology and logic. In a natural way, the problems surrounding the interconnection of science and theology became one of the Circle's subjects of interest.

When OBI began its activities, its members had little knowledge of this Krakowian tradition. They unwittingly continued it – likely thanks to Kraków's genius loci. The revival of the tradition owes much to the then-bishop of Kraków, Karol Wojtyła, who organized common seminars for philosophers, theologians and the representatives of the sciences.  

Within OBI, interdisciplinary research of a particular kind is conducted: OBI's slogan is 'philosophy in science', which boils down to tracing the philosophical issues involved in scientific theories. It is characteristic of their philosophical undertakings that their work leads to both new questions and areas of research and this is clearly visible in the case of OBI. The traditional problems of the interconnection of science and philosophy quickly gave rise to research concerning some more specific subjects, such as particular mathematical and physical theories and their philosophical implications, issues connected with evolutionary theory and its history, particular problems of logic and methodology, and the rapidly expanding questions surrounding neuroscience. In those investigations, the history of science was of particular help as an important means for understanding the phenomenon of science.

Such a broad scope of research interests leads firmly to many questions concerning the mutual relation between science and theology and the history of science is filled with such issues. However, the members of OBI were interested in such questions irrespective of their historical relevance, as OBI was affiliated with a theological university. Thus, the problems belonging to 'science and religion' became OBI's second main area of research.

The idea of establishing a new interdisciplinary center emerged as a response to the expansion of OBI's projects that began to surpass its organizational capabilities. The necessity arose to formalize the research groups, as well as to institutionalize all the activities. It is common that institutionalization destroys the enthusiasm of informal contacts and cooperation but all progress, however, bears other fruits: at some stage it may be necessary to make some risky decisions.

The first ideas which led to the development of the Center were put forward by Charles Harper of the Templeton Foundation, who believed that OBI should expand its activities to other Central and Eastern European countries. The members of OBI initially believed that such a task exceeded their organizational capabilities. However, the idea was simply one which would not go away.

The Templeton Foundation is mainly focused on the issues surrounding the new discipline of 'science and religion'. OBI, on the other hand, is interested in a broader field of interdisciplinary topics, of which 'science and religion' is only an important aspect. It is in terms of this more complex direction that the extension of OBI's activities was thought of.

At the end of the summer of 2007, the discussion concerning the establishment of a new institution (a center, a foundation or a society) entered a decisive stage, as a result of the conclusion of the 9th Methodological Conference in Kraków. The idea of establishing a joint-venture between OBI and the Jagiellonian University (UJ) emerged, which was fully supported by the rector of the Jagiellonian University, Professor Karol Musioł. A few months later a 'Steering Committee' was established, including the rector of the UJ Karol Musioł, the director of OBI Professor Michał Heller, Professor Andrzej Pelczar, Professor Jan Kozłowski, Professor Stanisław Wszołek (the Dean of the Philosophical Faculty of the Pontifical Academy of Theology), Professor Janusz Mączka and Dr. Jacek Urbaniec.

At the initial stages, the discussion within the Steering Committee concerned the institutional form of the future center. There were several possibilities: the Center could have been affiliated with one of the faculties of the Jagiellonian University, established as an inter-faculty institution or as an inter-university organization. It is the latter option that was finally chosen. The name of the new institution, the Copernicus Center, was not a subject of controversy but there are many organizations in Poland that bear the name of Copernicus. Therefore, it was decided that the newly established center would be the 'Copernicus Center for Interdisciplinary Studies', a name that distinguishes it from other Polish institutions, as well as indicating close ties with the Center for Interdisciplinary Studies (OBI). Moreover, It was decided that the Center would be a self-financing organization.

In March 2008 Rev. Professor Michał Heller was announced as the laureate of the 2008 Templeton Prize and he decided to dedicate the Prize to the creation of the Copernicus Center. In May 2008, during the Prize-awarding ceremonies in London, the rectors of the Jagiellonian University and of the Pontifical Academy of Theology met with the representatives of the Templeton Foundation to discuss the future of the Center and the best way to support its activities.

The procedure of establishing the Copernicus Center began in June 2008, when the Senates of both universities, UJ and PAT, agreed to create the Center. On July 10, 2008 an agreement between PAT and UJ was signed and, in September 2008, the statute of the Center was approved. At the same time the decree establishing the Center and appointing Rev. Professor Michał Heller as its first Director was issued by the rectors of UJ and PAT.

The Copernicus Center opening ceremony took place on October 2, 2008, in Collegium Maius of the Jagiellonian University. Speeches were delivered by Professor Karol Musioł, rector of the Jagiellonian University, Rev. Professor Jan M. Dyduch, rector of the Pontifical Academy of Theology, and Charles Harper, vice-president of the Templeton Foundation. Rev. Professor Michał Heller presented the ideas, the goals and the plans of the newly established Center.

The following day, 3 October 2008, there was a two-day conference, organized jointly by the Faculty of Physics, Astronomy and Applied Information Technology of the Jagiellonian University and the Faculty of Philosophy of the Pontifical Academy of Theology to honor the laureate of the Templeton Prize, Rev. Professor Michał Heller. The title of the conference was 'Will Science Replace Religion?'

In order to support the activities of the Copernicus Center, the Copernicus Center Foundation was established, with Rev. Professor Janusz Mączka as its president, and Marcin Gorazda, attorney at law, as its vice-president.