In the JBR, scholarly journals only are subject to evaluation. The initial list of the journals to be monitored and evaluated was established in 2003 in the procedure adopted by the responsible ministry and its bodies (expert committees). The list of the evaluated journals has been expanded in the meantime. New journals are added to the list annually. Decisions regarding the inclusion and suspension of journals are guided by the criteria defined in the document General Criteria for the Selection of Local Journals, published by the CEON/CEES, which complies with the Act on Editing Scholarly Journals, adopted by the ministry responsible for science.

For all rated journals, the indicators of impact and the compliance with European publishing standards (DOAJ, DOI and CC licences / defined user rights) are determined. The legitimacy of papers and the compliance with international ethical standards related to plagiarism and manipulative citation practices are checked, while bibliometric quality is established only for the journals subject to quality control in the national citation index.

If it is discovered while preparing the JBR that a journal has violated publishing ethical standards, a notification accompanied with appropriate documentation is sent to the editorial board and the journal is temporarily suspended from the list of evaluated journals. Once the reasons for suspension are resolved (e.g. by publishing corrections or retractions of disputed papers), the journal is re-evaluated in the following annual report. The journals that ignore the notifications are permanently suspended from the JBR.