An automatic system for measurement of CO2 efflux from soil and woody tissue (SAMTOC) was constructed in the Laboratory of Ecological Physiology of Forest Trees, Institute of Landscape Ecology, Academy of Sciences of the Czech Republic. The system SAMTOC is based on closed gas exchange system and consists of personal computer with control software, two infrared gas analysers, sampling change-over valves, eight soil chambers and eight woody tissue chambers and control units for chamber closing. The system measures courses of soil and woody tissue CO2 efflux and soil and woody tissue temperature. Fully automatic system SAMTOC is able to collect data during a whole vegetation season. It has been used in a Norway spruce stand at the Experimental Study Site Bílý Kříž in Beskydy Mountains since beginning of vegetation season 2001. The system underestimates soil and woody-tissue efflux about 5% and 8% respectively.