The feasibility to predict transition for three dimensional configurations is presented by means of a coupled program system consisting of a 3D Navier-Stokes solver, a transition module and a stability code. The assumption to use inviscid streamlines as integration paths for the N-factor calculation makes it possible to use linear stability theory in a straightforward way for three dimensional flows. The developed transition module has been adapted to be used with sequential and parallel computations to account for the increased computational demand for three dimensional configurations. Detailed investigations have been carried out, to show the ability of the Navier-Stokes code to provide data of three dimensional boundary layers of high accuracy needed for the stability analyses. Applications of the transition prediction method using the 2N-factor method for the case of an inclined prolate spheroid shows reasonably good results compared to experiments. First application of the transition prediction tool on a generic transport aircraft show promising results for the ability to predict transition on complex geometries.