Quantifying net carbon (C) storage by forests is a necessary step in the validation of carbon sequestration estimates and in assessing the possible role of these ecosystems in offsetting fossil fuel emissions. In eastern North America, five sites were established in deciduous forests to provide measurements of net ecosystem CO2 exchange (NEE) using micro-meteorological methods, and measures of major carbon pools and fluxes, using a combination of forest mensurational, eco-physiological, and other biometric methods. The five study sites, part of the AmeriFlux network, ranged across 10° of latitude and 18° of longitude, but were all of similar age, canopy height, and stand basal area. Here we present a cross-site synthesis of annual carbon storage estimates, comparing meteorological and biometric approaches, and also comparing biometric estimates based on analyses of autotrophic carbon pools and heterotrophic carbon fluxes (net ecosystem production, NEP) versus those based on measurements of change in two major carbon pools (ΔC). Annual above-ground net primary production (ANPP) varied nearly two-fold among sites and was strongly correlated with average annual temperature and with annual soil nitrogen mineralization (Nmin). Estimates of NEP ranged from 0.7 Mg C per hectare per year in northern lower Michigan to 3.5 Mg C per hectare per year in central Indiana, and were also well correlated with Nmin. There was less variation among sites in estimates of ΔC (range, 1.8–3.2 Mg C per hectare per year). In general, ΔC more closely matched NEE than did NEP, but there was no systematic pattern among sites in over- versus under-estimation of the biometric compared to the meteorologically based measures. Root and soil carbon dynamics were significant sources of uncertainty in our biometric measures and represent a prerequisite area of study needed for accurate estimates of forest carbon storage.