The role of the atmospheric boundary layer (ABL) in the atmosphere-climate system is the exchange of heat, mass and momentum between ‘the earth’s surface’ and the atmosphere. Traditionally, it is understood that turbulent transport is responsible for this exchange and hence the understanding and physical description of the turbulence structure of the boundary layer is key to assess the effectiveness of earth-atmosphere exchange. This understanding is rooted in the (implicit) assumption of a scale separation or spectral gap between turbulence and mean atmospheric motions, which in turn leads to the assumption of a horizontally homogeneous and flat (HHF) surface as a reference, for which both physical understanding and model parameterizations have successfully been developed over the years. Over mountainous terrain, however, the ABL is generically inhomogeneous due to both thermal (radiative) and dynamic forcing. This inhomogeneity leads to meso-scale and even sub-meso-scale flows such as slope and valley winds or wake effects. It is argued here that these (sub)meso-scale motions can significantly contribute to the vertical structure of the boundary layer and hence vertical exchange of heat and mass between the surface and the atmosphere. If model grid resolution is not high enough the latter will have to be parameterized (in a similar fashion as gravity wave drag parameterizations take into account the momentum transport due to gravity waves in large-scale models). In this contribution we summarize the available evidence of the contribution of (sub)meso-scale motions to vertical exchange in mountainous terrain from observational and numerical modeling studies. In particular, a number of recent simulation studies using idealized topography will be summarized and put into perspective – so as to identify possible limitations and areas of necessary future research.