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Avian haemosporidians are a common and widespread group of vector-borne parasites capable of infecting most bird species around the world. They can negatively affect host condition and fitness. Vultures are assumed to have a very low prevalence of these blood parasites, likely due to their strong immunity; however, factors contributing to variation in host exposure and susceptibility to haemosporidians are complex, and supporting evidence is still very limited. We analyzed blood samples collected from nestlings of three vulture species in Spain over 18 years, and used updated nested-PCR protocols capable of detecting all haesmosporidian cytochrome b lineages typical for diurnal birds of prey (Accipitriformes). Similarly to previous studies, we found low haemosporidian prevalence in cliff-breeding species, with Leucocytozoon as the only represented blood parasite genus: 3.1% in griffon vultures (Gyps fulvus) (n = 128) and 5.3% in Egyptian vultures (Neophron percnopterus) (n = 114). In contrast, the tree-breeding cinereous vulture (Aegypius monachus) had a substantially higher prevalence: 10.3% (n = 146). By far the most common lineage in Spanish scavenging raptors was the Leucocytozoon lineage CIAE02. No effects of nestling age and sex, or temporal trends in prevalence were found, but an effect of nest habitat (tree-nest vs. cliff-nest) was found in the griffon vulture. These patterns may be explained by a preference of vectors to forage in and around trees rather than on cliffs and wide open spaces. We found an apparent detrimental effect of haemosporidians on body mass of nestling cinereous vultures. Further research is needed to evaluate the pathogenicity of each haemosporidian lineage and their interaction with the immune system of nestlings, especially if compromised due to pollution with pharmaceuticals and infection by bacterial and mycotic pathogens.