A Reynolds-averaged Navier-Stokes solver, a laminar boundary-layer code and different transition prediction methods for the prediction of Tollmien-Schlichting and cross flow instabilities were coupled for the automatic prediction of laminar-turbulent transition on general 3-dimensional aircraft configurations during the ongoing computation of the flow. The prediction procedure is applied to a two-dimensional three-element high-lift airfoil configuration which is characterized by the existence of laminar separation bubbles using different operation modes of the procedure