Predicting when future species extinctions will occur is necessary for directing conservation investments but has proved difficult. We developed a new method for predicting extinctions over time, accounting for the timing and magnitude of habitat loss. We applied this to the Brazilian Amazon, predicting that local extinctions of forest-dependent vertebrate species have thus far been minimal ( 1% of species by 2008), with more than 80% of extinctions expected to be incurred from historical habitat loss still to come. Realistic deforestation scenarios suggest that local regions will lose an average of nine vertebrate species and have a further 16 committed to extinction by 2050. There is a window of opportunity to dilute the legacy of historical deforestation by concentrating conservation efforts in areas with greatest debt.