Tropical peatlands occupy 8% of the global peatland area and are recognised as a significant carbon store; holding a carbon pool of 50 Gt. Peat forms when inundation of water prevents the aerobic decomposition of plant materials, which accumulate and form peat. Traditionally these areas have been difficult to farm and are sparsely populated so have become economically attractive for agronomical purposes. This study investigated the implications of the peatland conversion process with respect to two greenhouse gases that have received less attention than carbon dioxide; nitrous oxide and methane. An 18 month study measured nitrous oxide and methane fluxes using the closed static chamber method from three sites representative of the land use change process occurring in Indonesia. These sites were a mixed peat swamp forest, a drained and logged forest and an industrial oil palm. Nitrous oxide and methane fluxes from the peat swamp forest were divided into hummocks and hollows, from the oil palm divided into the fertilized and unfertilized zone.