In this paper, the results of computational studies on the unsteady flow features in three-dimensional empty cavities and cavities with a representative store are presented. Flow simulations with a turbulence model based on a hybrid method, which behaves as a standard Reynolds-averaged Navier-Stokes (RANS) model within the attached boundary layer and as a Large-Eddy Simulation LES sub-grid scale model in the rest of the flow (commonly known as Detached-Eddy Simulation (DES)) are used in this study. The time-mean flow study showed the presence of three-dimensional effects inside the cavities. The mean flowfield visualisation also clearly showed the presence of a pair of ‘tornado-like’ vortices in the upstream half of the cavity which merge to a single, large recirculation further downstream. Visualisation for the cavity-with-store case revealed that the mean flowfield was effectively divided into two halves with significant reduction of the spanwise flow across the cavity width. In the unsteady flow study, near-field acoustic spectra were computed for the empty cavity and cavity-with-store cases. Study of unsteady pressure spectra for the cavity-with-store case found the presence of many peaks and the corresponding mode frequencies were found to agree well with the Rossiter modes. The blockage effect of store and strut on the spanwise flow is thought to have reduced the interaction, and subsequent non-linear coupling, between the Rossiter modes. This may be the reason for the co-existence of multiple modes without the coupling among them.