Respiration supports growth and maintenance processes and returns a substantial portion of the CO(2) fixed by photosynthesis to the atmosphere each year. Investigating stem respiration using CO(2) flux measurements is complicated by uncertainty surrounding the source of CO(2) diffusing from tree stems. Over 2 years we measured the stem efflux from 24 trees exposed to ambient or elevated CO(2). The rate of stem CO(2) efflux increased with annual tree diameter increment and the estimated uptake of dissolved CO(2) from the soil. To determine the source of CO(2) diffusing from tree stems, we used the fumigation gas at the Duke Forest Atmosphere Carbon Transfer and Storage-1 elevated-CO(2) experiment as a (13)C tracer and measured the presence of soil CO(2) in stem efflux on a subset of these trees. The isotopic composition of soil CO(2) explained a considerable portion of the variation in the composition of CO(2) in stem efflux. We also found that direct measurements of the isotopic composition of phloem-respired CO(2), unlike the CO(2) found in stem efflux, was less variable and distinct from the isotopic composition of soil CO(2). Tree growth rates and soil CO(2) concentrations found at the site together explained 56% of the variance in stem CO(2) efflux among trees. These results suggest that the uptake of CO(2) dissolved in soil water and transported through the vascular system can potentially confound efforts to interpret stem efflux measurements in trees exposed to elevated CO(2) and that previous studies may have overestimated the effects of elevated CO(2) on autotrophic respiration in tree stems.