Subsurface drainage systems (pipe/tile drain systems) in paddy fields have been used in Japan since the 1960s for appropriate water management to encourage rice growing. Water management using the drainage systems probably accelerates the aerobic decomposition of organic matter in the paddy soils, and the management using the systems also accelerates leaching of water-soluble fractions in the soils. To evaluate these side-effects of the drainage systems on methane (CH4) production potential in the soils, soil samples taken from four pairs of paddy fields with or without drainage systems (D-soils and ND-soils, respectively) were compared. In general, total C and N, hot-water-extractable hexose, ammonification and Fe2+ production were lower in D-soils than in ND-soils. Decomposition of buried rice straw during a fallow period was also accelerated in D-soils. Hence, both electron acceptors, such as reducible Fe, and electron donors, such as easily decomposable organic matter, in D-soils decreased on a short-term and long-term basis. To compare the effect of decreased electron acceptors and donors on the same criterion (mg C-eq kg(-1) dry matter (d.m.)), the oxidative capacity (OxiC) and reductive capacity (RedC) in each soil were calculated from the soil chemical and biological properties. Both OxiC and RedC decreased in D-soils, but the rate of decrease in RedC was 2.7-fold higher than that of OxiC. As the soil conditions became relatively oxidative, CH4 production potential in D-soils decreased by approximately 40%. Thus, the installation of subsurface drainage systems under poorly drained paddy fields relatively decreased RedC in soil, and that CH4 production potential in the soil also decreased.