Methane emitted at different plant conditions through the different organs of rice plants was studied using a closed chamber technique under the laboratory, phytotron, and greenhouse conditions in order to clarify and quantify the role of different organs of rice plant as methane emission sites. Rice plants grown in flooded soils emit methane to the atmosphere via the aerenchyma of leaves, nodes and panicles. Emission through the rice plants is controlled by diffusion. No methane is emitted via the transpiration stream. Leaves are the major release sites at the early growth stage while nodes become more important later. Cracks and porous structure were found in the nodes. Panicles generally contribute little to methane emission. Increasing water depth temporarily reduces methane emission while concentration gradients in rice plants readjust to unsubmerged emission sites. Methane emissions in rice plants cease only when the plants become totally submerged.