Laboratory columns (80 cm long, 10 cm diameter) of peat were constructed from samples collected from a subarctic fen, a temperate bog and a temperate swamp. Temperature and water table position were manipulated to establish their influence on emissions of CO2 and CH4 from the columns. A factorial design experiment revealed significant (P < 0.05) differences in emission of these gases related to peat type, temperature and water table position, as well as an interaction between temperature and water table. Emissions of CO2 and CH4 at 23°C were an average of 2.4 and 6.6 times larger, respectively, than those at 10°C. Compared to emissions when the columns were saturated, water table at a depth of 40 cm increased CO2 fluxes by an average of 4.3 times and decreased CH4 emissions by an average of 5.0 times. There were significant temporal variations in gas emissions during the 6-week experiment, presumably related to variations in microbial populations and substrate availability. Using columns with static water table depths of 0, 10, 20, 40 and 60 cm, CO2 emissions showed a positive, linear relation with depth, whereas CH4 emissions revealed a negative, logarithmic relation with depth. Lowering and then raising the water table from the peat surface to a depth of 50 cm revealed weak evidence of hysteresis in CO2 emissions between the falling and rising water table limbs. Hysteresis (falling > rising limb) was very pronounced for CH4 emissions, attributed to a release of CH4 stored in porewater and a lag in the development of anaerobic conditions and methanogenesis on the rising limb. Decreases in atmospheric pressure were correlated with abnormally large emissions of CO2 and CH4 on the falling limb. Peat slurries incubated in flasks revealed few differences between the three peat types in the rates of CO2 production under aerobic and anaerobic conditions. There were, however, major differences between peat types in the rates of CH4 consumption under aerobic incubation conditions and CH4 production under anaerobic conditions (bog > fen > swamp), which explain the differences in response of the peat types in the column experiment.