The stability of hypersonic boundary layers over flat plates and cones is analyzed using CFD simulations of the mean flows and linear stability analysis of the boundary layer profiles. Blowing and suction effects on disturbance amplification rates and predicted transition locations are investigated. In the case of blowing gas into the flow over a cone, it is found that the computational results match the trends observed in the experiments of increasing instability with increasing blowing rate. Next for the case of blowing, both reacting and non-reacting gases are considered, and the possible stabilizing effect of chemical reactions is investigated. Stability analyses are performed for small rates of CO2 injection into a low-enthalpy air flow, and the results show only slight disturbance amplification. Further analysis is required to see if CO2 injection into flows at higher enthalpies can have a more significant effect.