ImportanceLong-term control of SARS-CoV-2 requires effective vaccination strategies. This has been challenged by public mistrust and spread of misinformation regarding vaccine safety. Hence, better understanding and communication on the longer-term and comparative experiences of general population individuals following SARS-CoV-2 vaccination are required. ObjectiveTo evaluate and compare self-reported adverse effects following SARS-CoV-2 vaccination, participants perceptions regarding vaccinations and their compliance with recommended public health measures. Design, Setting and ParticipantsPopulation-based longitudinal cohort of 575 adults, randomly selected from all individuals presenting to the reference vaccination center of the Canton of Zurich, Switzerland, for receipt of BNT162b2, mRNA1273, or JNJ-78436735. ExposuresBNT162b2, mRNA1273, or JNJ-78436735 vaccines. Main Outcomes and MeasuresPrimary outcomes included period prevalence, onset, duration, and severity of self-reported adverse effects over 12 weeks following vaccination with a specific focus on the proportion of participants reporting allergic reactions, menstrual irregularities, or cardiac adverse effects, or requiring hospitalization. Secondary outcomes included risk factors associated with reporting adverse effects, perception of vaccine importance, trust in public health authorities and pharmaceutical companies, and compliance with recommended public health measures. Results454 (79.0%) participants reported at least one adverse effect during 12 weeks after vaccination. Prevalence was highest among mRNA-1273 recipients (88.7% vs. 77.3% after BNT162b2, 69.1% after JNJ-78436735). Most adverse effects were systemic (72%), occurred within 24 hours (67.9%), and resolved in less than three days (76.3%). 85.2% were reported as mild or moderate. Allergic reactions were reported by 0.4% of participants, hospitalizations by 0.7%, cardiac adverse effects by 1.4%. Menstrual irregularities were reported by 9% of female participants younger than 50 years. Female sex, younger age, higher education, and receipt of mRNA-1273 were associated with reporting adverse effects. Compared to JNJ-78436735 recipients, a higher proportion of mRNA vaccine recipients agreed that vaccination is important (87.5% vs. 28.5%), and trusted public health authorities (80.2% vs. 30.3%) and pharmaceutical companies (71.7% vs. 23.6%). Conclusions and RelevanceOur population-based cohort provided real-world data on self-reported adverse effects following SARS-CoV-2 vaccination and highlights the importance of transparent communication regarding adverse effects and building trust in public health authorities to ensure successful future vaccination campaigns. Main PointsOur representative population-based cohort study demonstrated the safety of three SARS-CoV-2 vaccines and provides real-world estimates on adverse effect incidence.Transparent communication of expected adverse effects to vaccine-seeking individuals is pivotal to build trust in current or future vaccination campaigns.