As land use change (LUC), including deforestation, is a patchy process, estimating the impact of LUC on carbon emissions requires spatially accurate underlying data on biomass distribution and change. The methods currently adopted to estimate the spatial variation of above- and below-ground biomass in tropical forests, in particular the Brazilian Amazon, are usually based on remote sensing analyses coupled with field datasets, which tend to be relatively scarce and often limited in their spatial distribution. There are notable differences among the resulting biomass maps found in the literature. These differences subsequently result in relatively high uncertainties in the carbon emissions calculated from land use change, and have a larger impact when biomass maps are coded into biomass classes referring to specific ranges of biomass values. In this paper we analyze the differences among recently-published biomass maps of the Amazon region, including the official information used by the Brazilian government for its communication to the United Nation Framework on Climate Change Convention of the United Nations. The estimated average pre-deforestation biomass in the four maps, for the areas of the Amazon region that had been deforested during the 1990–2009 period, varied from 205 ± 32 Mg ha−1 during 1990–1999, to 216 ± 31 Mg ha−1 during 2000–2009. The biomass values of the deforested areas in 2011 were between 7 and 24 % higher than for the average deforested areas during 1990–1999, suggesting that although there was variation in the mean value, deforestation was tending to occur in increasingly carbon-dense areas, with consequences for carbon emissions. To summarize, our key findings were: (i) the current maps of Amazonian biomass show substantial variation in both total biomass and its spatial distribution; (ii) carbon emissions estimates from deforestation are highly dependent on the spatial distribution of biomass as determined by any single biomass map, and on the deforestation process itself; (iii) future deforestation in the Brazilian Amazon is likely to affect forests with higher biomass than those deforested in the past, resulting in smaller reductions in carbon dioxide emissions than expected purely from the recent reductions in deforestation rates; and (iv) the current official estimate of carbon emissions from Amazonian deforestation is probably overestimated, because the recent loss of higher-biomass forests has not been taken into account.