A simulation model based on satellite observations of monthly vegetation greenness from the Moderate Resolution Imaging Spectroradiometer (MODIS) was used to estimate monthly carbon fluxes in terrestrial ecosystems of Brazilian Amazon and <i>Cerrado</i> regions over the period 2000–2002. The NASA-CASA (Carnegie Ames Stanford Approach) model estimates of annual forest production were used for the first time as the basis to generate a prediction for the standing pool of carbon in above-ground biomass (AGB; g C m^&minus;2) for forested areas of the Brazilian Amazon region. Plot-level measurements of the residence time of carbon in wood in Amazon forest from Malhi et al. (2006) were interpolated by inverse distance weighting algorithms and used with CASA to generate a new regional map of AGB. Data from the Brazilian PRODES (Estimativa do Desflorestamento da Amazônia) project were used to map deforested areas. Results show that net primary production (NPP) sinks for carbon varied between 4.25 Pg C yr^&minus;1 (1 Pg=10¹⁵ g) and 4.34 Pg C for the region and were highest across the eastern and northern Amazon areas, whereas deforestation sources of CO₂ flux from decomposition of residual woody debris were higher and less seasonal in the central Amazon than in the eastern and southern areas. Increased woody debris from past deforestation events was predicted to alter the net ecosystem carbon balance of the Amazon region to generate annual CO₂ source fluxes at least two times higher than previously predicted by CASA modeling studies. Variations in climate, land cover, and forest burning were predicted to release carbon at rates of 0.5 to 1 Pg C yr^&minus;1 from the Brazilian Amazon. When direct deforestation emissions of CO₂ from forest burning of between 0.2 and 0.6 Pg C yr^&minus;1 in the Legal Amazon are overlooked in regional budgets, the year-to-year variations in this net biome flux may appear to be large, whereas our model results implies net biome fluxes had actually been relatively consistent from year to year during the period 2000–2002. This is the first study to use MODIS data to model all carbon pools (wood, leaf, root) dynamically in simulations of Amazon forest deforestation from clearing and burning of all kinds.