We report the finding of tick-borne encephalitis (TBE)-virus in indigenous Ixodes ricinus (L.), ‘Candidatus Neoehrlichia mikurensis’ in exotic Ixodes frontalis (Panzer) and Rickettsia aeshlimannii in exotic Hyalomma marginatum Koch subadult ticks detached from 18.5% (107/577) infested migratory birds in the Baltic region of Russia. This is the first record of human pathogenic ‘Candidatus N. mikurensis’ in I. frontalis ticks. Moreover, seven other pathogens were identified in I. ricinus ticks. Spotted Fever Group rickettsiae were the predominant pathogen group and were detected only in nymphs. Future investigations are warranted to further characterize the role of birds in the epizootiology of tick-borne pathogens in this region.