During the growing season, nighttime ecosystem respiration emits 30–100% of the daytime net photosynthetic uptake of carbon, and therefore measurements of rates and understanding of its control by the environment are important for understanding net ecosystem exchange. Ecosystem respiration can be measured at night by eddy covariance methods, but the data may not be reliable because of low turbulence or other methodological problems. We used relationships between woody tissue, foliage, and soil respiration rates and temperature, with temperature records collected on site to estimate ecosystem respiration rates at six coniferous BOREAS sites at half-hour or 1-hour intervals, and then compared these estimates to nocturnal measurements of CO2 exchange by eddy covariance. Soil surface respiration was the largest source of CO2 at all sites (48–71%), and foliar respiration made a large contribution to ecosystem respiration at all sites (25–43%). Woody tissue respiration contributed only 5–15% to ecosystem respiration. We estimated error for the scaled chamber predictions of ecosystem respiration by using the uncertainty associated with each respiration parameter and respiring biomass value. There was substantial uncertainty in estimates of foliar and soil respiration because of the spatial variability of specific respiration rates. In addition, more attention needs to be paid to estimating foliar respiration during the early part of the growing season, when new foliage is growing, and to determining seasonal trends of soil surface respiration. Nocturnal eddy covariance measurements were poorly correlated to scaled chamber estimates of ecosystem respiration (r2=0.06–0.27) and were consistently lower than scaled chamber predictions (by 27% on average for the six sites). The bias in eddy covariance estimates of ecosystem respiration will alter estimates of gross assimilation in the light and of net ecosystem exchange rates over extended periods.