An aircraft aeroelasticity measurement system according to the invention can be used to perform in-flight wing twist measurements of an aircraft or any moving vehicle or structure on which its sensors can be mounted. The system includes a centralized processing unit, a reference navigation unit mounted in the aircraft body, a plurality of measurement navigation units mounted in the aircraft wings, and a global positioning system ("GPS") receiver that generates GPS data for enhancing the accuracy of the navigation data. The system collects navigation data from the reference navigation unit and the measurement navigation units, generates navigation solutions from the navigation data, and performs a stochastic alignment and flexure estimation procedure to generate a corrected measurement solution that indicates the aeroelasticity of the aircraft. Wing twist and wing deflection information can be derived from the corrected measurement solution.