Haemosporidian blood parasites are frequent amongst passerines. Though they often do not cause detectable consequences to host health, however, their presence or absence and also their prevalence across host populations may potentially carry meaningful information about the health, stress, body condition and viability of bird individuals or populations. The study of migratory birds captured in Eilat, Israel, allowed us to evaluate the prevalence of blood parasite infections in a wide range of both migrant and resident species in spring (N = 1,950) and autumn (N = 538) of 2004 and 2005. According to blood film microscopy, Haemoproteus spp. and Leucocytozoon spp. were more prevalent in the spring than in the autumn (0.289, 0.082 vs. 0.132, 0.033, respectively), whilst Plasmodium spp. exhibited a slight opposite trend (0.034, 0.056). All other parasites (such as trypanosomes, microfilaria and haemococcidians) were rare. During the spring seasons, prevalences were significantly higher in migrant than in resident species, whilst this difference was only marginally significant in the autumn. Given that Eilat is a migration hotspot for several Palearctic passerine species, the present descriptive study may hopefully serve to set the baseline values for future long-term epidemiological monitoring.