This paper presents a new method to measure wing deflections in flight for small UAVs. It employs a pair of high resolution stereo cameras and LED wing markers, as well as a small form factor computer for control and storage. Post-processing of all the data is done off-line. Accuracy benchmark tests are conducted. Finally, theoretical discussion of wing shape reconstruction is presented. The method employs numerical optimization by minimizing the difference between numerical geometrically nonlinear slender beam equations and observed markers points with associated uncertainties.Nomenclature c x ,c y = principal focal point C = circularity d = disparity e = error metric f x ,f y = focal length (in pixels) F = focal length F i ,M i = design variables (point forces and moments in UM/NAST) J = cost functional k 1 ,k 2 ,k 3 = radial distortion parameters k = nodal points where point forces and moments are applied N = number of marker points p 1 ,p 2 = tangential distortion parameter p i = beam deflection computed by UM/NAST q i = measured beam deflection Q = reprojection matrix r = radial distance R = rotation matrix t = translational vector T x = x component of rotation matrix x,y = image coordinates (distorted) x c ,y c = image coordinates (pin hole model) X,Y,Z = physical coordinates X cb,i = known checkerboard coordinates σ i = error weight