The technique of numerical simulation of receptivity and stability for hypersonic boundary-layers using the in-house code HSFlow (High-Speed Flow solver) is presented. It is based on direct modeling of propagation of artificial disturbances by unsteady compressible Navier–Stokes equations. Presented is the overview of results obtained using this technique for 2D near-wall flows over flat and grooved plate, sharp cone, rounded compression corner, porous surface at freestream Mach 5–6. Also demonstrated are preliminary results of ongoing 3D DNS on flat plate. The simulations are conducted for high-frequency forcing, which excites unstable disturbances in the boundary layer relevant to the second-mode instability, which is the first stage of the laminar-turbulent transition process. The calculations illustrate high robustness of the technique, which allows for simulation of nonlinear dynamics of disturbance fields in flows with essential spatial irregularities.