Estimating dynamic terrestrial ecosystem carbon (C) sources and sinks over large areas is difficult. The scaling of C sources and sinks from the field level to the regional level has been challenging due to the variations of climate, soil, vegetation, and disturbances. As part of an effort to estimate the spatial, temporal, and sectional dimensions of the United States C sources and sinks (the U.S. Carbon Trends Project), this study estimated the forest ecosystem C sequestration of the Appalachian region (186,000 km²) for the period of 1972–2000 using the General Ensemble Biogeochemical Modeling System (GEMS) that has a strong capability of assimilating land use and land cover change (LUCC) data. On 82 sampling blocks in the Appalachian region, GEMS used sequential 60 m resolution land cover change maps to capture forest stand-replacing events and used forest inventory data to estimate non-stand-replacing changes. GEMS also used Monte Carlo approaches to deal with spatial scaling issues such as initialization of forest age and soil properties. Ensemble simulations were performed to incorporate the uncertainties of input data. Simulated results show that from 1972 to 2000 the net primary productivity (NPP), net ecosystem productivity (NEP), and net biome productivity (NBP) averaged 6.2 Mg C ha⁻¹ y⁻¹ (±1.1), 2.2 Mg C ha⁻¹ y⁻¹ (±0.6), and 1.8 Mg C ha⁻¹ y⁻¹(±0.6), respectively. The inter-annual variability was driven mostly by climate. Detailed C budgets for the year 2000 were also calculated. Within a total 148,000 km² forested area, average forest ecosystem C density was estimated to be 186 Mg C ha⁻¹ (±20), of which 98 Mg C ha⁻¹ (±12) was in biomass and 88 Mg C ha⁻¹ (±13) was in litter and soil. The total simulated C stock of the Appalachian forests was estimated to be 2751 Tg C (±296), including 1454 Tg C (±178) in living biomass and 1297 Tg C (±192) in litter and soil. The total net C sequestration (i.e. NBP) of the forest ecosystem in 2000 was estimated to be 19.5 Tg C y⁻¹ (±6.8).