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To reveal the prevalence of spotted fever group (SFG) rickettsiae and Babesia sp. in Ixodes ricinus (L.) ticks from migratory birds, 236 specimens represented 8 species of Passeriformes and were collected at Curonian Spit in Kaliningrad enclave of North-Western Russia. The ticks (total 126) being detached from four bird species, Turdus philomelos, Fringilla coelebs, Parus major, and Sturnus vulgaris, were investigated by PCR using the primers Rp CS.877p/Rp CS.1258n for the detection of Rickettsia and BJ1/BN2 for Babesia spp. Babesia spp. were detected in 2 of 126 (1.6%) ticks. The partial sequence of 18S rDNA had 100% similarity to human pathogenic Babesia sp. EU1. The SFG rickettsiae were detected in 19 of 126 (15.1%) ticks collected from the above-mentioned bird species. BLAST analysis of SFG rickettsia gltA assigned sequences to human pathogenic Rickettsia helvetica (10.3%), Rickettsia monacensis (3.9%), and Rickettsia japonica (0.8%) with 98%-100% sequence similarity. The SFG rickettsiae and Babesia sp. EU1 in ticks collected from the passerines in Russia were detected for the first time. The survey indicates that migratory birds may become a reservoir for Babesia spp. and SFG rickettsiae. Future investigations need to characterize the role of birds in the epidemiology of these human pathogens in the region.