Introduction Since 2017, the University Campus Library of Masaryk University in Brno, Czech Republic (UCL) has been providing a service to check compliance with the principles of transparency and best practice in scholarly journals. The service is provided exclusively to PhD students and researchers from CEITEC, Faculty of Sports Studies, Faculty of Medicine and departments of Faculty of Science situated in the University Campus at Bohunice. Method From February 2017 to March 2018, journals were evaluated on the basis of the COPE, DOAJ, OASPA, WAME and Jeffrey Beall’s criteria. During this period, it was found that some of the criteria were not relevant, and thus the method used to uncover suspicious journals and publishers was revised. Since April 2018, the service has adopted overlapping criteria issued only by widely respected authorities, namely COPE, DOAJ, OASPA and WAME. Results From February 2017 to November 2018, we were requested 166 times by 44 users to check 157 journals. We spent 73.5 hours in analysing journals, and of these journals 52 (31.3%) were evaluated as very disputable, 10 (6.0%) as rather disputable, 26 (15.7%) as rather indisputable, 76 (45.8%) as indisputable and 2 (1.2%) as unverifiable. The most frequent breaches of publication ethics were a peer-review time that was not specified or short (70), article processing charges that were not specified or non-transparent (62), a missing or insufficient declaration of manner of Open Access (39), no e-mail service contact or a general one (31), false information about metrics from Web of Science and Scopus (26), failure to adhere to periodicity in the last three years (25), declaration of misleading metrics (25), no editor-in-chief (24), a fake person in the editorial board (23), or having a name similar to a previously published journal (20). Discussion From the point of view of financial and personnel requirements, using the service was, so far, more efficient than using the commercial database Cabells Scholarly Analytics. During the autumn of 2018, we arranged two workshops to discuss the relevance of the criteria mentioned above. Participants identically indicated an archiving of full texts, a declaration of compliance with ethical standards, a description of the peer-review process, a specific amount of article processing charges and valid information about metrics from Web of Science and Scopus as the important criteria. According to the experience gained and the results of the workshops, we will try to specify the principles of transparency and best practice in scholarly journals not only on the basis of the discussion of professional organisations and librarians but on statistical analysis as well. Conclusion Our two-year experience with the service “Compliance with the principles of transparency and best practice in scholarly journals” shows the vital role of libraries in the evaluation of journals and in supporting researchers in choosing journals for their publications.