Evolutionary biologists have paid much attention to studies of parasite-host interactions. The prevalence of blood parasites is highly dependent on diagnostic methods, season, and regions. Recently, polymerase chain reaction (PCR) based molecular diagnostic methods have been developed to detect the infection of blood parasites. In order to reevaluate the prevalence of blood parasites in Japanese passerines, I compared the prevalence of blood parasites found by microscopic examination with that found by PCR-based molecular diagnostics. 14.5% of individuals (225 of 1553) were infected with avian malaria, and 25.1% of individuals (220 of 878) were infected with avian trypanosome in Japan. The present study showed significantly higher prevalence of trypanosomes than previously reported. The trypanosome might represent a suitable agent for studying host-parasite interactions in birds, because it affects both growth and fitness. PCR-based molecular diagnostics revealed a higher prevalence of both avian malaria and trypanosome in the present study than in previous ones. The PCR-based molecular diagnostic method is more effective than microscopic examination for screening for infection of blood parasites, if the primes of a target parasite are available.