Measurements of land-surface emission rates of greenhouse and other gases at large spatial scales (10 000 m2) are needed to assess the spatial distribution of emissions. This can be readily done using spatial-integrating micro-meteorological methods like flux-gradient methods which were evaluated for determining land-surface emission rates of trace gases under stable boundary layers. Non-intrusive path-integrating measurements are utilized. Successful application of a flux-gradient method requires confidence in the gradients of trace gas concentration and wind, and in the applicability of boundary-layer turbulence theory; consequently the procedures to qualify measurements that can be used to determine the flux is critical. While there is relatively high confidence in flux measurements made under unstable atmospheres with mean winds greater than 1 m s-1, there is greater uncertainty in flux measurements made under free convective or stable conditions. The study of N2O emissions of flat grassland and NH3 emissions from a cattle lagoon involves quality-assured determinations of fluxes under low wind, stable or night-time atmospheric conditions when the continuous "steady-state" turbulence of the surface boundary layer breaks down and the layer has intermittent turbulence. Results indicate that following the Monin-Obukhov similarity theory (MOST) flux-gradient methods that assume a log-linear profile of the wind speed and concentration gradient incorrectly determine vertical profiles and thus flux in the stable boundary layer. An alternative approach is considered on the basis of turbulent diffusivity, i.e. the measured friction velocity as well as height gradients of horizontal wind speeds and concentrations without MOST correction for stability. It is shown that this is the most accurate of the flux-gradient methods under stable conditions.