The purpose of this paper is to describe a methodology for identifying different operational consequences and associated costs caused by aircraft system failure, in order to facilitate and enhance the capability of taking correct and efficient decisions when analyzing the cost-effectiveness of maintenance tasks. The paper focuses on the operational consequences of failures that lead to delay. To identify the operational consequences of aircraft system failures, Empirical studies of possible scenarios involving aircraft failures and their operational consequences for a commercial airline have been performed. Empirical data were extracted through document studies and interviews, guided by the application of an Event Tree Analysis (ETA). In order to effectively utilize the knowledge of field experts in the assessment process, a pairwise comparison technique was adopted for quantifying the contribution of different factors to the operational. The work was performed together with experienced practitioners from both an aircraft manufacturer and commercial airlines, which contributed to a continuous verification of the outcome of the study.The study shows that the proposed methodology based on ETA and pairwise comparison can be used to identify and quantify the cost of operational consequences of failures in aircraft operation, when there is no sufficient and reliable data.