This study’s objectives were to investigate factors affecting the adverse events of the COVID-19 vaccine in Indonesia among health care workers and compare adverse events following SARS-CoV-2 vaccine using CoronaVac as the first and second dose and Moderna used as the booster third dose. A cross-sectional study was conducted using the Self-reporting Online Survey Platform (Google Form) from August to October 2021. Subjects included in the study were ENT specialists and residents all over Indonesia who had been vaccinated with both doses of CoronaVac COVID-19 vaccine and Moderna COVID-19 vaccine as a booster dose. Among a total of 1394 participants, 51.2% and 43.7% of subjects experienced adverse events following the first and second dose of the CoronaVac vaccine. Adverse events are significantly higher following the third dose of Moderna vaccine (95.3%) with p-value <0.001, odds ratio (OR) 26.63 (95% CI 19.87-35.7). Adverse events following the CoronaVac vaccine were significantly higher in females and individuals with comorbidities in the first dose (p=0.002 and p=0.04), and the second dose (p=0.008 and p=0.042). Adverse events following the Moderna vaccine were significantly higher in females (p=0.01) and lower in individuals ≥40 years of age (p=0.017). Comorbidity status did not affect adverse events following the Moderna vaccine.