An accurate estimate of carbon fluxes associated with tropical deforestation from the last two decades is needed to balance the global carbon budget. Several studies have already estimated carbon emissions from tropical deforestation, but the estimates vary greatly and are difficult to compare due to differences in data sources, assumptions, and methodologies. In this paper, we review the different estimates and datasets, and the various challenges associated with comparing them and with accurately estimating carbon emissions from deforestation. We performed a simulation study over legal Amazonia to illustrate some of these major issues. Our analysis demonstrates the importance of considering land-cover dynamics following deforestation, including the fluxes from reclearing of secondary vegetation, the decay of product and slash pools, and the fluxes from regrowing forest. It also suggests that accurate carbon-flux estimates will need to consider historical land-cover changes for at least the previous 20 years. However, this result is highly sensitive to estimates of the partitioning of cleared carbon into instantaneous burning vs. long-timescale slash pools. We also show that carbon flux estimates based on ‘committed flux’ calculations, as used by a few studies, are not comparable with the ‘annual balance’ calculation method used by other studies.