Wind and temperature data collected on commercial airliners are used to investigate the effects of underlying terrain on mesoscale variability. These results expand upon those of Nastrom et al., by including all available data from the Global Atmospheric Sampling Program (GASP) and by more closely focusing on the coupling of variance with the roughness of the underlying terrain over mountainous regions. The earlier results, showing that variances are larger over mountains than over oceans or plains, with greatest increases at wavelengths below about 80 km, are confirmed. Statistical tests are used to confirm that these differences are highly significant. Over mountainous regions the roughness of the underlying terrain was parameterized from topographic data and it was found that variances are highly correlated with roughness and, in the troposphere, with background wind speed. Average variances over the roughest terrain areas range up to about ten times larger than those over the oceans. These results are found to follow the scaling with stability predicted in the framework of linear gravity wave theory. The implications of these results for vertical transports of momentum and energy, assuming they are due to gravity waves and considering the effects of intermittency and anisotropy, are also discussed.