To separate CO2 efflux from roots (Rr) and soil (Rs), we developed a system to measure Rr continuously. Using this system, seasonal variation in Rr was obtained in a temperate forest in Japan. We measured Rs, CO2 efflux from mineral soil (Rm) and environmental factors simultaneously, and the characteristic and seasonality of Rr were analysed in comparison with Rs. Rr and Rs showed different responses to soil water content: Rs decreased with decreasing soil water content, whereas Rr peaked at relatively low soil water content. Rr/Rs decreased from 64.8% to 27.3% as soil water content increased from 0.075 to 0.225 cm cm-3. The relationship between respiration and temperature appears to change seasonally in response to phenological and biological factors. Rr showed clear seasonal variation as a function of soil temperature. During the growing period, Rr exhibited a higher rate at the same soil temperature than during other periods, which may be due to phenological influences such as fine root dynamics. Rs decreased during the summer despite high soil temperatures. The seasonal peak for Rs occurred earlier than that for soil temperature. Rr/ Rs ranged between 25% and 60% over the course of the year. 2006 The Authors Journal compilation © 2006 Blackwell Munksgaard.