Thanks to a considerable pool of potential mentors and qualified researchers, as well as relatively modern research equipment, the RBI is an attractive place for doctoral studies for the best students from Croatian universities and ensures a flow of high-quality doctoral students.

In cooperation with certain universities in Croatia, the RBI has established several doctoral and specialised study programmes on the basis of agreements with various universities in Croatia, and RBI scientists are also actively involved in undergraduate teaching.

The strongest cooperation is with the University of Zagreb, with which a formal cooperation agreement was signed in 2007. Prominent teaching activities take place at the Faculty of Natural Sciences and Mathematics as well as at the Faculties of Electronics and Computer Science, Agriculture and Medicine. In cooperation with the Josip Juraj Strossmayer University in Osijek, an interdisciplinary postgraduate degree programme in "Nature and Environmental Protection" was established in 2002, which has been run as a doctoral and specialist degree programme since 2008 and accepts an average of 10 doctoral students and 15 specialist students each year.

Together with the Josip Juraj Strossmayer University and the University of Dubrovnik, the RBI initiated the joint interdisciplinary doctoral programme in Molecular Biosciences in 2006, in which an average of 40 students enrol each year.

In cooperation with the Universities of Split, Dubrovnik and Zadar, the RBI launched a postgraduate doctoral programme in Biology of Neoplasms in 2006. On the basis of a cooperation agreement with the Faculty of Medicine at the University of Zagreb, the RBI participates in the postgraduate doctoral programme in Biomedicine and Healthcare and the doctoral programme in Neurosciences.

On the basis of mutual cooperation agreements with the Faculty of Natural Sciences of the University of Zagreb, the Institute of Marine and Coastal Areas of the University of Dubrovnik and the Institute of Oceanography and Fisheries in Split, the Ruđer Bošković Institute has been involved in the joint implementation of the interdisciplinary postgraduate university programme in Oceanology since 2006. In 2010, the RBI started a joint doctoral programme in Chemistry of the Mediterranean Environment with the University of Split.

On the basis of a cooperation agreement signed in 2007 with the Juraj Dobrila University in Pula, the Ruđer Bošković Institute organises a university postgraduate programme in marine sciences, in which RBI scientists teach a total of 72 courses. In the same year, an agreement was signed with the University of Rijeka to start an undergraduate, postgraduate and doctoral programme in the field of medicinal chemistry. The first part of this joint programme, the Undergraduate University Study - Biotechnology and Drug Research, at the Department of Biotechnology at the University of Rijeka, accepted 40 students in the 2009/2010 academic year. It is particularly worth mentioning that the research assistants at the Institute were also involved in teaching during this period, especially in leading practical courses, laboratory exercises and seminars. From 2006 to 2010, 89 RBI research assistants were involved in the delivery of 116 courses, including 58 undergraduate courses, 33 graduate courses and 25 doctoral and specialist courses.

It is important to emphasise that the RBI established the first postgraduate study programme in the field of natural sciences in the former Yugoslavia as early as 1957. RBI's vision for the next 5-10 years is to become a national and regional centre for postgraduate education in specific scientific activities of the Institute. The Institute's human and infrastructural resources will be geared towards establishing international doctoral studies in English, with RBI scientists playing a leading role, but also collaborating with colleagues from domestic and foreign universities and scientific institutes. In addition to its own studies, the RBI will participate as an equal partner with universities in Croatia and abroad in joint study programmes and doctoral studies.