We have used FTIR spectroscopy for high precision trace gas analysis combined with micrometeorological flux-gradient and chamber methods to measure the fluxes of trace gases CO2, CH4, N2O and CO between agricultural soils and the atmosphere. In flux gradient measurements, vertical profiles of the trace gases were measured every 30 minutes from the ground to 22 m. When combined with independent micrometeorological measurements of heat, water vapour and radiative fluxes, trace gas fluxes from the underlying surface could be determined. In chamber measurements, a closed chamber was placed over the soil surface and the air in the chamber monitored continuously by FTIR spectroscopy. Fluxes were calculated from the time rate of change of concentrations in the chamber after closure. The FTIR measurements were fully automated and ran reliably for several weeks, routinely obtaining precision of 0.1-0.5%.