Birds contain greater diversity of Haemosporidian parasites than any other vertebrate and these parasites are most notably represented by three genera: Plasmodium, Haemoproteus, and Leukocytozoon. Birds are thus a uniquely informative model to study the phylogeny of such parasites. Recent studies revealed that while many birds infected with these parasites are asymptomatic, their fitness is impacted , especially when the parasite is coupled with a second infection or environmental stressors. The two common methods of screening for these parasites are nested PCR or blood-film microscopy, both of which are time and resource consuming as well as low throughput. This study employed an innovative use of quantitative PCR (qPCR) to screen for these three parasite genera with a single assay in golden eagles and can be easily adapted to screen for specific strains or amplify the product for cloning. This study determined that use of qPCR provides a sensitive, high throughput, and easily adaptable method to not only screen for infection but determine help determine the strain of the infecting parasite and the relative parasite load.