We examined blood smears from 139 Northern Saw-whet Owls (Aegolius acadicus) to ascertain the prevalence of haematozoa in this species during fall migration in eastern North America. Owls were captured with mist nets on the Mohonk Preserve near New Paltz, New York from 1 October to 2 December 2011. We examined blood smears under an optical microscope at 200× and 1000× magnification, and observed four genera of haematozoa, Haemoproteus, Leucocytozoon, Plasmodium, and Trypanosoma, in addition to a genus or genera of microfilarial nematodes, unidentifiable by morphology. We found haematozoa in blood smears from both male and female Northern Saw-whet Owls and in both age groups sampled, i.e., hatching year and after hatching year. Leucocytozoon was the most common parasite, with an overall prevalence of 49.6%. Prevalence of Haemoproteus, microfilaria, Plasmodium, and Trypanosoma was 5.0%, 5.0%, 10.0%, and 2.9% respectively, and overall occurrence of infection was 64%. We found no difference in body condition of individuals compared by age, infection status, or intensity of infection. To our knowledge, this is the first record of Plasmodium in Northern Saw-whet Owls, and the first study to document five genera of haematozoa in Northern Saw-whet Owls during fall migration. Revealing new host–parasite information, this study contributes to the information portfolio of Northern Saw-whet Owls and, thus, may influence future research.