This thesis considers the stability and transition of incompressible boundary layers. In particular, the Falkner–Skan–Cooke boundary layer subject to a cylindrical surface roughness, and the Blasius boundary layer with applied localized suction are investigated. These flows are of great importance within the aviation industry, feature complex transition scenarios, and are strongly three-dimensional in nature. Consequently, no assumptions regarding homogeneity in any of the spatial directions are possible, and the stability of the flow is governed by an extensive three-dimensional eigenvalue problem. The stability of these flows is addressed by high-order direct numerical simulations using the spectral element method, in combination with a Krylov subspace projection method. Such techniques target the long-term behavior of the flow and can provide lower limits beyond which transition is unavoidable. The origin of the instabilities, as well as the mechanisms leading to transition in the aforementioned cases are studied and the findings are reported. Additionally, a novel method for computing the optimal forcing of a dynamical system is developed. This type of analysis provides valuable information about the frequencies and structures that cause the largest energy amplification in the system. The method is based on the inverse power method, and is discussed in the context of the one-dimensional Ginzburg–Landau equation and a two-dimensional flow case governed by the Navier–Stokes equations. / <p>QC 20151015</p>