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Background In next fall and winter, SARS-CoV-2 could circulate in parallel with seasonal influenza. The dual epidemics will result in considerable morbidity and mortality; therefore, influenza vaccination may be essential. Recent studies found increased risk of coronavirus in individuals receiving influenza vaccination. Aims Our aim is to analyse the association between influenza vaccination and COVID-19 in a population of healthcare workers (HCWs). Methods IgG antibodies against SARS-CoV-2 were detected in 3520 HCWs at a large hospital in Northern Italy. For each participant, we collected data on flu immunization status for the last five flu seasons. Logistic regression was used to test associations between seasonal flu vaccination status and a positive serology tests for COVID-19. Results During the last five flu seasons, 2492 vaccinations were administered. Serology tests were negative for 3196 (91%) HCWs and residents and only 21 (1%) people had an equivocal test (12.0–15.0 AU/mL). Only 128 (4%) people received a diagnosis of COVID-19, with a positive swab test. No flu vaccinations for the last five flu seasons were specifically associated with diagnosis of COVID-19 or with positive results of serology tests. Conclusions Flu vaccinations did not appear to be associated with SARS-CoV-2 infection. Influenza vaccination should continue to be recommended for HCWs and for individuals at increased risk for severe illness from respiratory infection.