The lowland peatlands of south-east Asia represent an immense reservoir of fossil carbon and are reportedly responsible for 30% of the global carbon dioxide (CO2) emissions from Land Use, Land Use Change and Forestry. This paper provides a review and meta-analysis of available literature on greenhouse gas fluxes from tropical peat soils in south-east Asia. As in other parts of the world, water level is the main control on greenhouse gas fluxes from south-east Asian peat soils. Based on subsidence data we calculate emissions of at least 900 g CO2 m−2 a−1 (∼250 g C m−2 a−1) for each 10 cm of additional drainage depth. This is a conservative estimate as the role of oxidation in subsidence and the increased bulk density of the uppermost drained peat layers are yet insufficiently quantified. The majority of published CO2 flux measurements from south-east Asian peat soils concerns undifferentiated respiration at floor level, providing inadequate insight on the peat carbon balance. In contrast to previous assumptions, regular peat oxidation after drainage might contribute more to the regional long-term annual CO2 emissions than peat fires. Methane fluxes are negligible at low water levels and amount to up to 3 mg CH4 m−2 h−1 at high water levels, which is low compared with emissions from boreal and temperate peatlands. The latter emissions may be exceeded by fluxes from rice paddies on tropical peat soil, however. N2O fluxes are erratic with extremely high values upon application of fertilizer to wet peat soils. Current data on CO2 and CH4 fluxes indicate that peatland rewetting in south-east Asia will lead to substantial reductions of net greenhouse gas emissions. There is, however, an urgent need for further quantitative research on carbon exchange to support the development of consistent policies for climate change mitigation.