Hypersonic gas flow over cones is solved using computational fluid dynamics to obtain accurate boundary layer profiles. A linear stability analysis is performed on the profiles to determine the amplification rates of naturally occurring disturbances, and this information is used with the eN method to predict the boundary layer transition location. The effects of free-stream total enthalpy and chemical composition on transition location are studied to give a better understanding of recent experimental observations. Namely, there is an increase in transition Reynolds number with increasing free-stream total enthalpy, and this increase is greater for gases with lower dissociation energies. The results show that linear stability predicts the same trends that were observed in the experiments, but with N = 10, it consistently overpredicts the transition Reynolds numbers by about a factor of 2. The results of numerical experiments are presented which show the effect of reaction endo- or exothermicity on disturbance amplification rates.