Respiration in forest tree stems is an important component of the global carbon cycle. This respiration is traditionally estimated by measurements of the CO2 efflux from the stem. However, recent studies have suggested that movement of CO2 in the transpiration stream causes large errors in the respiration estimated by the CO2 efflux. Here we demonstrate a new approach for determining the ratio of respiration to CO2 efflux, which is based on specially designed chambers, and combined CO2 and O2 measurements. The high accuracy O2 measurement is performed by mass spectrometric measurement of the O2/Ar ratio. Testing the method gave repeatable results which point that in some conditions up to 40% of the respired CO2 can be carried away from the site of respiration.