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Background: The United Nations warned of COVID-19 related mental health crisis; however, it is unknown whether there is an increase in prevalence of mental disorders as existing studies lack a reliable baseline analysis. We aimed to analyse trends in the prevalence of mental disorders prior to and during the COVID-19 pandemic. Methods: We analysed data from repeated cross-sectional surveys on a representative sample of non-institutionalized Czech adults (18 to 64 years) from both 2017 and 2020. We used Mini International Neuropsychiatric Interview (MINI) as the main screening instrument. We calculated descriptive statistics and utilized regression to compare the prevalence of current mood and anxiety disorders, suicide risk, and alcohol related disorders at baseline and during the peak of Covid-19 related lockdown. Results: We found an increased proportion of those experiencing symptoms of at least one current mental disorder during the COVID-19 pandemic by more than 10 % when compared to the baseline in November 2017 (19.76, 95% CI = 18.38; 21.12 in 2017 vs 30.62, 95% CI = 28.96; 32.24 in 2020). The prevalence of both major depressive disorder (3.96, 95% CI = 3.28; 4.62 vs 11.88, 95% CI = 10.72; 13.04); and suicide risk (3.88, 95% CI = 3.21; 4.52 vs 12.28, 95% CI = 11.06; 13.44) tripled and current anxiety disorders almost doubled (6.88, 95% CI = 6.01; 7.73 vs 13.51, 95% CI = 12.28; 14.7). The prevalence rate of alcohol use disorders in 2020 was approximately the same as in 2017 (10.84, 95% CI = 9.78; 11.89 vs 10.63, 95% CI = 9.5; 11.72); however, there was a significant increase in weekly binge drinking behaviors (4.07% vs 6.39%). Strong worries about both, health or economic consequences of COVID-19, were associated with an increased odds of having a mental disorder (1.62, 95% CI = 1.4; 1.88 and 1.43, 95% CI = 1.25; 1.64 respectively). Interpretation: This study provides evidence matching concerns that COVID-19 related mental health problems is a real and major threat to populations. This finding emphasizes an urgent need to scale up mental health promotion and prevention globally. Funding Statement: The study was supported by the project the project “Sustainability for the National Institute of Mental Health”, LO1611, Ministry of Education, Youth and Sports of the Czech Republic under the NPU I program. Declaration of Interests: Authors declare that they have no conflict of interest. Ethics Approval Statement: This study was approved by the Ethics Committee of the National Institute of Mental Health, Czech Republic (registration number 127/20). All respondents provided oral informed consent and, at the end of the interview, they were informed about the emergency hotline providing psychological aid to Czech residents during the COVID-19 pandemic.