Nocturnal ecosystem respiration, estimated by micrometeorological methods (Fc + Fstor), is dominated by fluxes (Fc) under more turbulent conditions, and by storage in the canopy air space (Fstor) under calm conditions. In a ponderosa pine ecosystem in Oregon, calm nocturnal conditions (defined here as u* < 0.25 m s-1) occurred at least 70% of the time during 1996. The low-turbulence observations are usually excluded from further analysis and replaced with estimates from empirical relationships (e.g. soil temperature and fluxes under more turbulent conditions). Scaled-up chamber estimates of soil CO2 fluxes, foliage and wood respiration (Fch) were moderately correlated with change in CO2 storage in the canopy (Fstor) on calm nights (R2 = 0.60). On windy nights (u* > 0.25 m s-1), the sum of turbulent flux measured above the canopy by eddy covariance and Fstor was only weakly correlated with summed chamber estimates (R2 = 0.14); the eddy covariance estimates were lower than chamber estimates by 50%. The apparent underestimation of nocturnal fluxes by eddy covariance could be due to observational problems associated with stable conditions that generally occur at night (e.g., failure of instrument to resolve small scale eddies), and analysis-related issues (e.g. intermittent turbulence). Annual estimates of net ecosystem exchange will be strongly influenced by the method chosen to estimate nocturnal fluxes.