Background: While the uptake of the COVID-19 vaccine among healthcare workers (HCWs) is suboptimal, vaccine hesitancy has not been characterized in detail in this population. Objective: The aim of this study was to compare the prevalence of health-related conditions reported by HCWs during the COVID-19, 2020/21 flu, and 2019/20 flu vaccination campaigns, so to test the hypothesis that HCWs were more prone to report health conditions during the COVID-19 campaign. Methods: We analyzed vaccination questionnaires of 176 hospital-based HCWs who underwent the COVID-19 and the 2020/21 flu vaccinations; 2019/20 flu vaccination questionnaires were available for 130 of them. Outcomes included self-reported allergies, chronic diseases, and use of medications. We tested for prevalence equality, analyzed differences using the kappa statistics and concordance correlation, and explored factors associated with differences in reporting. Results: There was no difference in the proportion of HCWs reporting allergies in the three questionnaires, while chronic diseases were more frequently reported in the COVID-19 than in both 2020/21 (p = 0.04) and 2019/20 flu questionnaires (p = 0.02). Furthermore, a higher proportion of HCWs reported medications use in the COVID-19 vaccination questionnaire, compared to both the 2020/21 and the 2019/20 flu vaccination questionnaires (p < 0.001 for both). In each vaccine campaign, women reported more conditions than men, and the difference between chronic disease reports was greater for women than for men. Conclusions: Our results show more frequent reporting of health conditions during the COVID-19 than the flu vaccination campaigns, providing quantitative evidence of hesitancy of HCWs towards the COVID-19 vaccine.