Standing biomass is a major, often poorly quantified determinate of carbon losses from land clearing. We analyzed maps from the 2001–2007 PRODES deforestation time series with recent regional pre-deforestation aboveground biomass estimates to calculate carbon emission trends for the Brazilian Amazon basin. Although the annual rate of deforestation has not changed significantly since the 1990s (ANOVA, p = 0.3), the aboveground biomass lost per unit of forest cleared increased from 2001 to 2007 (183 to 201 Mg C ha⁻¹; slope of regression significant: p < 0.01). Remaining unprotected forests harbor significantly higher aboveground biomass still, averaging 231 Mg C ha⁻¹. This difference is large enough that, even if the annual area deforested remains unchanged, future clearing will increase regional emissions by ∼0.04 Pg C yr⁻¹ – a ∼25% increase over 2001–2007 annual carbon emissions. These results suggest increased climate risk from future deforestation, but highlight opportunities through reductions in deforestation and forest degradation (REDD).