ABSTRACT The Gyrfalcon (Falco rusticolus) is a top avian predator, an Arctic specialist, and among the bird species most vulnerable to climate change. This vulnerability is driven by their narrow ecological niche, limited or lack of southward migration, and circumpolar distribution where the most rapid climatic changes are occurring. Climatic and habitat changes may alter Gyrfalcon disease ecology due to changes in vector distributions, host ranges, and pathogen life cycles. Warmer Arctic temperatures and accompanying landscape changes may also alter the Gyrfalcon’s prey base, and dietary habits can influence transmission of pathogens. To better understand disease ecology in Gyrfalcons, we compared pathogen prevalence across varying time periods at three study sites in Alaska—the Seward Peninsula (2014–2022), the Alaska Peninsula (2021–2022), and the Yukon–Kuskokwim Delta (2008–2013). We collected Gyrfalcon whole blood, thin blood films, cloacal swabs, and fecal samples for serology, haemoparasite assays, microbiological cultures, and fecal tests for parasites. An aliquot of whole blood preserved on filter paper or in Longmire solution was kept for molecular diagnosis of haemoparasites. Serology revealed high exposure to Salmonella (77%), low seroprevalence of avian influenza antibodies (1.5%), exposure to falcon adenovirus type 1 in hatch-year Gyrfalcons (1.3%), and the first report of a Leucocytozoon spp. blood parasite in a Gyrfalcon. We found no antibodies indicative of prior exposure to avian paramyxovirus, West Nile virus, or Chlamydia. One nestling and one hatch-year bird sampled (2 of 12) on the Seward Peninsula exhibited oral plaques from capillarids (Eucoelus spp.) in contrast to those trapped in the Izembek National Wildlife Refuge on the Alaska Peninsula (0 of 6).