This study derives from and extends the discussions of a US DOE sponsored workshop held on 30 and 31 May, 2000 in Boulder, CO concerning issues and uncertainties related to long-term eddy covariance measurements of carbon and energy exchanges. The workshop was organized in response to concerns raised at the 1999 annual AmeriFlux meeting about the lack of uniformity among sites when making spectral corrections to eddy covariance flux estimates and when correcting the eddy covariance CO2 fluxes for lack of energy balance closure. Ultimately, this lack of uniformity makes cross-site comparisons and global synthesis difficult and uncertain. The workshop had two primary goals: first, to highlight issues involved in the accuracy of long-term eddy covariance flux records; and second, to identify research areas and actions of high priority for addressing these issues. Topics covered at the workshop include different methods for making spectral corrections, the influence of 3D effects such as drainage and advection, underestimation of eddy covariance fluxes due to inability to measure low frequency contributions, coordinate systems, and nighttime flux measurements. In addition, this study also covers some new and potentially important issues, not raised at the workshop, involving density terms to trace gas eddy covariance fluxes (Webb et al., 1980). Wherever possible, this paper synthesizes these discussions and make recommendations concerning methodologies and research priorities.