It is well known that most fluid flows observed in nature or encountered in engineering applications are turbulent and involve separation. Fluid flows in turbines, diffusers and channels with sudden expansions are among the widely observed areas where separation substantially alters the flow field and gives rise to complex flow dynamics. Such types of flows are referred to as internal flows since they are confined within solid surfaces and predominantly involve the generation or utilization of mechanical power. However, there is also a vast variety of engineering applications where the fluid flows past solid structures, such as the flow of air around an airplane or that of water around a submarine. These are called external flows and as in the former case the downstream evolution of the flow field is crucially influenced by separation. The present doctoral thesis addresses both internal and external separated flows by means of direct numerical simulations of the incompressible Navier-Stokes equations. For internal flows, the wall-driven flow in a onesided expansion channel and the pressure-driven flow in a plane channel with a single thin-plate obstruction have been studied in the fully developed turbulent state. Since such geometrical configurations involve spatially developing turbulent flows, proper inflow conditions are to be employed in order to provide a realistic fully turbulent flow at the input. For this purpose, a newly developed technique has been used in order to mimic an infinitely long channel section upstream of the expansion and the obstruction, respectively. With this approach, we are able to gather accurate mean flow and turbulence statistics throughout each flow domain and to explore in detail the instantaneous flow topology in the separated shear layers, recirculation regions as well as the recovery zones. For external flows, on the other hand, the flow past a prolate spheroid has been studied. Here, a wide range of Reynolds numbers is taken into consideration. Based on the characteristics of the vortical structures in the wake, the flow past a prolate spheroid is classified as laminar (steady or unsteady), transitional or turbulent. In each flow regime, the characteristic features of the flow are investigated by means of detailed frequency analysis, instantaneous vortex topology and three-dimensional flow visualizations.