Geopolitical conflicts, such as the annexation of Crimea and the ongoing war in Ukraine, may influence how author affiliations are reported in academic publishing. Listing Ukrainian cities under Russia can affect academic integrity and visibility. The aim of this study was to examine the prevalence and trends of Ukrainian cities designated as Russian in author affiliations. A retrospective analysis was conducted on PubMed articles from January 2014 to May 2024. Fifty major Ukrainian cities and 20 cities hosting leading medical universities were selected. Articles listing these cities under ‘Russia’ or ‘Ukraine’ were identified using proximity search queries and common transliterations. Irrelevant entries were excluded manually. Among 17,893 articles, 413 (2.3%) listed Ukrainian cities under Russia, mostly Simferopol and Sevastopol (91.8%). The rate increased steadily over time, peaking at 3.5% in 2022. In top-100 general internal medicine journals, 8 of 268 articles (3.0%) showed similar designations. These findings reflect the continued use of contested Russian designations for Ukrainian cities in academic publications.