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Infectious diseases can potentially affect the seasonal migration of hawks. We tested three species of California hawks from autumn 2004 to spring 2006 for haemosporidian blood parasites (Plasmodium, Haemoproteus, and Leucocytozoon spp.). We screened 323 Red-tailed Hawks (Buteo jamaicensis), 100 Cooper's Hawks (Accipiter cooperii), and 21 Red-shouldered Hawks (B. lineatus) for blood parasites using polymerase chain reaction (PCR). Among these hawks, 221 (50%) were infected with Haemoproteus, 134 (30%) with Leucocytozoon, and none with Plasmodium species. We compared blood parasite prevalence results to identify infection patterns in two populations (birds captured during autumn at a migration watchsite in the Marin Headlands [Golden Gate Raptor Observatory] vs. birds captured during winter in the Central Valley) and between years, seasonal periods, and sex and age classes. In 2004, Marin Red-tailed Hawks were more likely to test positive for blood parasites if sampled late in the migration; however, we observed the opposite pattern in Cooper's Hawks. The prevalence of both Haemoproteus and Leucocytozoon followed the same seasonal trends in each host species, which suggested a possible effect of infection status on raptor migration. We also observed different patterns of variation in parasite prevalence between years at the two sampling sites, but no significant differences between juvenile and adult birds at either site. In addition, using a simple measure of body condition, we observed significant differences between males and females with regard to the effects of parasite infection and sampling location. These results provide a baseline for future studies monitoring long-term changes in parasite prevalence and effects on California's migrating hawks.