The early detection of cracks, fatigue, corrosion, and structural failure in aging aircraft is one of the major challenges in the aircraft industry. Common inspection techniques are time consuming and hence can have strong economic implications due to aircraft downtime. As a result, during the past decade a number of methodologies have been proposed for detecting structural damage based on variations in the structure’s dynamic characteristics. This paper describes the implementation of the natural excitation technique (NExT) combined with the eigensystem realization algorithm (ERA) to determine the dynamic characteristics of a T-34A Mentor acrobatic category aircraft and a modified DC-3 cargo/transport category aircraft. In-flight acceleration data were processed using NExT-ERA to monitor the predominant natural frequencies and associated mode shapes of the aircraft for varying flight conditions. The results show the effectiveness of this modal identification methodology and the possibility of implementing it in a real-time structural health monitoring system for aircraft.