This paper reports on the significance of warping deformation on the stability analysis of a flexible cross-hinge mechanism, which consists of two leaf springs with rectangular cross-section. The effect of misalignments in this mechanism is studied analytically, numerically and experimentally. An analytical buckling analysis is carried out to determine the theoretical critical load of a generalized cross-hinge mechanism on the basis of first principles. A geometrically nonlinear beam finite element with a non-uniform torsion description is used to model the leaf springs numerically. The change in natural mode frequencies and stiffness as a function of the misalignment is determined by a multibody program. Measurements from a dedicated experimental set-up confirm that the inclusion of warping effects is crucial, even for narrow rectangular cross-sections: it is found that the effects of warping increase the analytical critical buckling load of the system by 55%.