Methane (CH4) is a particularly potent greenhouse gas with a radiative forcing 23 times that of CO2 on a per mass basis. Flooded rice paddies are a major source of CH4 emissions to the Earth's atmosphere. A free-air CO2 enrichment (FACE) experiment was conducted to evaluate changes in crop productivity and the crop ecosystem under enriched CO2 conditions during three rice growth seasons from 1998 to 2000 in a rice paddy at Shizukuishi, Iwate, Japan. To understand the influence of elevated atmospheric CO2 concentrations on CH4 emission, we measured methane flux from FACE rice fields and rice fields with ambient levels of CO2 during the 1999 and 2000 growing seasons. Methane production and oxidation potentials of soil samples collected when the rice was at the tillering and flowering stages in 2000 were measured in the laboratory by the anaerobic incubation and alternative propylene substrates methods, respectively. The average tiller number and root dry biomass were clearly larger in the plots with elevated CO2 during all rice growth stages. No difference in methane oxidation potential between FACE and ambient treatments was found, but the methane production potential of soils during the flowering stage was significantly greater under FACE than under ambient conditions. When free-air CO2 was enriched to 550 ppmv, the CH4 emissions from the rice paddy field increased significantly, by 38% in 1999 and 51% in 2000. The increased CH4 emissions were attributed to accelerated CH4 production potential as a result of more root exudates and root autolysis products and to increased plant-mediated CH4 emissions because of the larger rice tiller numbers under FACE conditions.