The largest extinction event in the Holocene occurred on Pacific islands, where Late Quaternary fossils reveal the loss of thousands of bird populations following human colonization of the region. However, gaps in the fossil record mean that considerable uncertainty surrounds the magnitude and pattern of these extinctions. We use a Bayesian mark-recapture approach to model gaps in the fossil record and to quantify losses of nonpasserine landbirds on 41 Pacific islands. Two-thirds of the populations on these islands went extinct in the period between first human arrival and European contact, with extinction rates linked to island and species characteristics that increased susceptibility to hunting and habitat destruction. We calculate that human colonization of remote Pacific islands caused the global extinction of close to 1,000 species of nonpasserine landbird alone; nonpasserine seabird and passerine extinctions will add to this total.