Aim: The study’s primary aim is to evaluate the frequency and distribution of 3rd dose vaccines’ side effects, especially for the rare heterologous vaccine scheme. The secondary objective is to determine the factors affecting the booster COVID-19 vaccination preferences of HCWs. MaterialandMethods:Thissingle-center,retrospectivedescriptivestudywasconductedon1058HCWs,throughanonlinesurvey. In this study, 3rd dose COVID-19 vaccine preferences, the affecting factors, and the side effects were questioned and analyzed. Results: 87% of the participants (n=921) had the 3rd booster COVID-19 vaccine. Of those vaccinated, 82.4% (n=759) had Pfizer/BioNTech, and 17.6% (n=162) had CoronaVac/Sinovac. The most common factors that affect the 3rd dose vaccine choice are physicians’/HCWs’ recommendations (53.4%; n=492), scientific publications (42.7%; n=393), and recommendations of the Ministry of Health (41.6 %, n=383). 83% (n=630) of 759 who were vaccinated with Pfizer/ BioNTech developed post-vaccine side effects, while 59% (n=96) of 162 HCWs who were vaccinated with CoronaVac/ Sinovac developed (p<0.001). The most common side effect observed was muscle-joint pain (49.2%), and it occurred most frequently in the first 48 hours after vaccination (36%). The most commonly reported side effects in the 2-7 days and 7-28 days post-vaccination were muscle-joint pain (11.6%) and fatigue (1.6%), respectively. It was observed that fatigue, headache, muscle-joint pain, local reaction at the injection site, fever, and lymphadenopathy side effects were more common in those who administered the Pfizer/BioNTech vaccine. Conclusion: Although it is associated with developing more frequent side effects, mRNA vaccines are preferred by HCWs. Physician/HCWs recommendations and scientific publications were found to be the most valuable sources on the decision of vaccine preference.