Measurements of the sources and sinks of biogenic trace gases such as N2O and CH4 from terrestrial ecosystems are important in explaining and predicting the influence of these gases on global warming. Because of their biological origins the fluxes of these gases often show high spatial and temporal variation. Traditional methods of flux measurement use different types of field chambers or micrometeorologically based methods. These methods have several shortcomings and may not always be applicable to flux measurements of trace gases such as N2O or CH4. Fourier transform infrared (FTIR) spectroscopy, due to its path-integrating and multicomponent nature, shows unique potential for the measurement of fluxes of greenhouse gases from various ecosystems. To assess this potential, we have used a medium resolution (1 cm-1) FTIR spectrometer to test its suitability for area-integrated measurements, simultaneous multicomponent measurements, and continuous real-time measurements of trace gas fluxes. We have tested three different configurations: a conventional field chamber where the FTIR is used to continuously and simultaneously monitor the concentration changes of several gases, a megachamber method using a large tent as field chamber with the FTIR optical path within the chamber, and a micrometeorological flux gradient method. The three configurations are described and discussed and their performance is demonstrated in measurements of fluxes of N2O from a fertilized grassland and CH4 from a forest soil.