A fundamental configuration that appears frequently on aerodynamic surfaces associated with high-speed flight vehicles (e.g. scramjet combustors, spacecraft hulls and thermal protection systems) is that of a cavity. Cavities significantly alter the local flow environment and can be a desirable or undesirable feature depending on the geometric features and operating conditions. For instance, cavities can occur by design to mitigate excessive temperatures associated with hypersonic flight. The focus of this work is to investigate hypersonic flow past deep cavities in the high-altitude rarefied flow regime. The direct simulation Monte Carlo (DSMC) method has been employed to numerically study the flow and thermal patterns. DSMC is a high-fidelity molecular-level method that can accurately capture both the near-continuum and low-density rarefied flow regimes. We will report flow and thermal characteristic for various degrees of flow rarefaction corresponding to different altitudes of a hypersonic flight vehicle.