Disease can have severe impact on animal populations, especially in rare species. Baseline data for atypical hostspecies are missing for a range of infectious diseases, although such hosts are potentially more affected than thenormal vectors and reservoir species. If highly pathogenic avian influenza strikes rare birds of prey, this mayhave crucial impact on the predator species itself, but also on the food web in which it interacts. Here we presentthe first large-scale screening of raptors that regularly consume birds belonging to the natural reservoir ofinfluenza A viruses. Influenza A virus prevalence was studied in two rare raptors, the white-tailed sea eagle(Haliaeetus albicilla) and the peregrine falcon (Falco peregrinus). Nestlings were screened for active (181 whitetailed sea eagles and 168 peregrine falcons) and past (123 white-tailed sea eagles and 6 peregrine falcons)infection in 2006–2007, and an additional 20 succumbed adult white-tailed sea eagles were sampled in 2003–2006. Neither high- nor low-pathogenic influenza infections were found in our sample, but this does not rule outthat the former may have major impact on rare raptors and their food webs.