The effects of rarefaction on hypersonic boundary layer flow over a discrete surface roughness element are examined in the context of the STS-119 flight experiment. The purpose of this flight experiment was to acquire data regarding the onset of roughnessinduced boundary layer transition during atmospheric entry of the Orbiter. Transition onset was confirmed at a freestream Mach number M∞=15. The height of the boundary layer trip k was determined to be approximately one-quarter of the boundary layer thickness d, and initial estimates indicate that the local Knudsen number (Kn=λ/k) in the region of the roughness was O(10-3), such that k≈450λ, where λ is the molecular mean free path. In this regime, the continuum approximations of zero velocity and no thermal slip at the wall begin to break down, and thermal non-equilibrium effects may become more prominent due to a relative increase in time required for thermal equilibration. The aim of this work is to address the significance of rarefaction effects in modeling the disturbance field generated by hypersonic boundary layer flow over surface roughness using a hybrid of the DAC and DPLR numerical simulation codes. Preliminary studies have been conducted to examine flow over the STS-119 boundary layer trip geometry under flight conditions at M∞=20. 3. A comparison of the flowfield quantities between the hybrid and DPLR solutions indicate good agreement in the general shock structure and expansion formed in the region of the roughness, and it was also observed that the disturbances of the flowfield quantities in the wake tend to be more pronounced in the DPLR solution. The total heat flux on the surface of the protuberance is also examined, and preliminary results indicate that the hybrid solution produces a peak heat flux that is approximately 10% lower than the peak heat flux predicted by DPLR.