Fish eagles (genus Haliaeetus) potentially have contributed the bones of their prey to many late Cenozoic concentrations of vertebrate microfossils. To evaluate possible biases in the taxa and skeletal elements preserved in assemblages accumulated by fish eagles, which could affect paleoecological and evolutionary interpretations derived from Cenozoic microfaunal localities, a sample of 1883 bones accumulated by modern African fish eagles (H. vocifer) was collected from a roost near Lake Turkana, Kenya. Characteristics of the bone assemblage include (1) taxonomic composition dominated by fish; (2) diverse but small-sized and ecologically restricted animals including inshore fish, aquatic birds, very small nocturnal mammals (which may have been contributed by other raptors), and small reptiles (possible predators on the roost); (3) poor survivorship for specific categories of skeletal elements; (4) considerable bone breakage for all but the smallest animals; and (5) a distinctive pattern of postcranial fragmentation for bird and mammal elements. The fish eagle element profile has some similarities to those of other diurnal raptors, but its cumulative signature can be distinguished from those of other bone accumulators and includes characteristics that would also be manifest in fossil assemblages. Examination of fossil microfaunas from the Plio-Pleistocene localities of Kanapoi (Kenya), Inolelo (Tanzania), and Olduvai Gorge (Tanzania) shows that the patterns of element preservation for Kanapoi and Inolelo do not match those of the Lake Turkana fish eagle roost. Nonetheless, some aspects of the Olduvai Gorge FLKN assemblage show taxonomic and skeletal similarities. In light of the selective choices of prey by fish eagles, the fauna recovered from Olduvai Gorge FLKN might not accurately reflect faunal diversity or patterns of abundance at this locality during the Pleistocene. Because fish eagles of the genus Haliaeetus are found on three continents, have a fossil record extending to the Miocene, and deposit bones in a habitat conducive to preservation, the taxa preserved at many other late Cenozoic microfaunal sites also might be biased. Therefore, taphonomic profiles of late Cenozoic microfaunal assemblages should be compared against the taphonomic profiles typical of fish eagle roosts before faunal characterizations of sites are applied in analyses of paleoecological evolution.