From consideration of the length scales characteristic of molecular and turbulent phenomena, it is proposed that flow instabilities and structural motions should be generated under certain rarefied, hypersonic flow conditions. This proposal is investigated using the direct simulation Monte Carlo (DSMC) method for hypersonic, rarefied flow over a cylinder. The overall mean flow field contains a number of regions including an undisturbed free stream, a bow shock, a recompression in the wake, and a recirculation zone behind the cylinder. Analysis of the fluctuations in velocity and number density predicted by the DSMC technique for this flow is conducted. An important aspect of this analysis is the clarification of the nature of the observed fluctuations. It is found that different types of fluctuations are found in the bow shock and in the wake. These are attributed to different types of physical phenomena. In the bow shock, large fluctuations are caused by the macroscopic field gradients in the shock front. In the wake, one can also observe an area with enhanced scatter of the mean flow characteristics caused by a macroscopic structural motion. The calculated instantaneous flow fields show small oscillations of the vortices immediately downstream of the cylinder for a Mach number of 26 and a Knudsen number of 0.0025. When the Knudsen number is reduced to 0.001, an irregular secondary flow motion containing vortex structures is exhibited in the far wake.