The design of vehicles which travel at hypersonic speeds is strongly determined by drag characteristics and heat transfer. A portion of this drag and heating is due to the boundary layer where viscosity and thermal conductivity are most important. The level of drag and heating depends on whether the boundary layer is laminar or turbulent with the latter leading to higher levels of drag and heating. In addition, as high speed boundary layers transition from laminar to turbulent flow, an overshoot of the heat transfer beyond that of turbulent flow has been observed in experiments. In low disturbance environments, transition to turbulence follows the path of receptivity, linear growth, nonlinear interaction, and finally breakdown to turbulence. The linear growth of disturbances can be determined by linear stability theory. An analysis of the predicted growth rates and integrated growth of linear disturbances for hypersonic boundary layers including thermal and chemical non-equilibrium is undertaken. The sensitivity to different chemical assumptions, transport models and thermal boundary conditions is investigated. A disturbance energy norm is proposed and its corresponding balance equation is derived. This energy norm is then to determine the effect of different terms of the linear stability equations and to compute transient growth for hypersonic laminar boundary layers. DNS (Direct Numerical Simulation) is used to simulate the nonlinear breakdown to turbulence for a variety of transition scenarios for both zero pressure gradient and adverse pressure gradient high-speed flat plate boundary layers in order to investigate the mechanism for the overshoot of heat transfer in transitional hypersonic boundary layers. The initial disturbances are excited through suction and blowing at the wall and their frequencies are chosen based on linear stability theory. Different transition mechanisms are investigated including a pair of oblique waves and 2D and 3D instabilities at higher frequencies which are unique to high speed boundary layers. Oblique breakdown shows a clear overshoot in heat transfer and skin friction and leads to a fully turbulent boundary layer. The alternative scenarios also lead to transition but further downstream and without large overshoots in heat transfer. A detailed analysis of the transitional and turbulent regions is undertaken.