Purpose:The purpose of this paper is to diagnose the impact of the epidemic threat on air transport as illustrated by the case of the SARS-CoV-2 epidemic, and to forecast possible changes in the civil aviation protection system. Design/Methodology/Approach: An analysis of the evolution of the world's passenger traffic since 1945 in the context of changes in the world's civil aviation security system shows that the two major events of the 9/11 attack and the SARS epidemic have brought a decrease in the number of passengers carried. While the 9/11 attack entailed deep changes in the security system, the SARS epidemic has not resulted in deployment of additional safety measures. The purpose of the methodology employed, based on a system analysis, a trend analysis and passenger surveys, was to forecast changes in the civil aviation security system. Findings: Empirical studies show that the current SARS-CoV-2 pandemic has been unprecedented in terms of a decrease in passenger numbers, so an analysis of the already deployed ad hoc changes as well as efforts to deploy additional security measures demonstrates the permanent character of those changes in the system of safeguarding civil aviation against epidemic threats. This conclusion is confirmed also by air passenger surveys. Practical Implications: The study has practical implications for the direction of changes in the civil aviation protection system in response to the epidemic threats and implementation of additional safeguards. Originality/value: The 9/11 terrorist attack brought changes in the global civil aviation security system. On the other hand, no lessons were learnt from the previous SARS epidemic and no additional safeguards were implemented against the epidemic threat. Interpretation of the study findings has allowed the authors to conclude that changes in the aviation system are made with respect to incurred events, and therefore an analysis of trends can be utilised in pro-active safety and security measures in the civil aviation.