Forested tropical peatlands in Southeast Asia store at least 42 000 Million metric tonnes (Mt) of soil carbon. Human activity and climate change threatens the stability of this large pool, which has been decreasing rapidly over the last few decades owing to deforestation, drainage and fire. In this paper we estimate the carbon dioxide (CO[subscript 2]) emissions resulting from drainage of lowland tropical peatland for agricultural and forestry development which dominates the perturbation of the carbon balance in the region. Present and future emissions from drained peatlands are quantified using data on peatland extent and peat thickness, present and projected land use, water management practices and decomposition rates. Of the 27.1 Million hectares (Mha) of peatland in Southeast Asia, 12.9 Mha had been deforested and mostly drained by 2006. This latter area is increasing rapidly because of increasing land development pressures. Carbon dioxide (CO[subscript 2]) emission caused by decomposition of drained peatlands was between 355 Mt y[superscript −1] and 855 Mt y[superscript −1] in 2006 of which 82% came from Indonesia, largely Sumatra and Kalimantan. At a global scale, CO[subscript 2] emission from peatland drainage in Southeast Asia is contributing the equivalent of 1.3% to 3.1% of current global CO[subscript 2] emissions from the combustion of fossil fuel. If current peatland development and management practices continue, these emissions are predicted to continue for decades. This warrants inclusion of tropical peatland CO[subscript 2] emissions in global greenhouse gas emission calculations and climate mitigation policies. Uncertainties in emission calculations are discussed and research needs for improved estimates are identified