A nonlinear approach is developed and used to predict crack initiation in discretely assembled composite panels made from skin and stringers. Particular emphasis is given to stringer run outs within a stiffened panel for the optimization of novel composite wing configurations. The nonlinear structural behavior is obtained by means of the von Karman formulation for moderately large deflections in plates; three-dimensional assemblies are schematized and the effect of eccentricity is included in the simulation. Solutions are calculated by means of a Rayleigh–Ritz approach based on Galerkin’s orthogonal eigenfunctions, and a linear elastic fracture mechanics-based model is used to simulate the crack initiation in the critical regions. Numerical results obtained by means of the present method are validated against tests reported in the literature and compared with advanced nonlinear finite element analysis. Limits of applicability and further potential exploitations are discussed. A validation study showed fairly good correlation with reported experimental data.