The net ecosystem exchange of carbon dioxide (NEE) between terrestrial ecosystems and the atmosphere is presently a subject of intense research around the world. NEE, measured from micrometeorological towers with the eddy covariance technique, provides a way to examine the biotic and abiotic controls on net carbon cycle processes. While we have learned much from application of eddy covariance, when used alone we are limited to analysis of net fluxes, the difference between carbon uptake by plants and release by all organisms. The addition of stable isotope measurements provides a way to partition NEE into its component processes, gross photosynthetic carbon uptake and total ecosystem respiration. The isotopic characteristics of whole-ecosystem photosynthesis and respiration were examined for 3 months in 2003 at a high-elevation coniferous forest (the Niwot Ridge AmeriFlux site), and combined with NEE and meteorological data collected simultaneously at the site. Using these datasets, the application of stable isotope methods to partition NEE will be discussed in detail.