This is dataset about Serbian papers published in journals indexed in Web of Science collections in the period 2003-2021 We used as "serbian" countries: Serbia, Serbia and Montenegro, Yugoslavia The terms Serbian researcher and Serbian paper used in this dataset are defined as follows: Serbian researcher is a researcher affiliated with a Serbian institution, Serbian paper is a paper with at least one Serbian researcher in the list of authors. This means that a paper published by a researcher with non-Serbian nationality (i.e. German) working at a Serbian institution is taken into account in the analysis of Serbian papers described in this paper. Thomson Reuters’ Web of Science (WoS) database was used for data acquisition. We searched Serbian papers in two WoS collections - Science Citation Index Expanded (SCIE) and the Social Science Citation Index (SSCI). The search query executed over those collections on 18th of January, 2022. CU=(%Serbia% OR %Serbia and Montenegro% OR %Yugoslavia%) AND PY=[2003-2021] We also analyzed the number of articles of Serbian researchers published in journals with an unstable impact factor (IF), i.e. journals which didn’t have an IF before 2008, and had one in some subperiod of 2008-2015, i.e. lost their IF until 2015. The majority of those journals stopped being indexed in Web of Science as a ban for losing the quality or having predatory journal behavior. We found 143 such journals and their ISSNs by using the JCR (Journal citation reports in the period 2007 - 2015).