Wild rodents have been implicated as natural reservoirs for the tick-borne agents. In Europe, rodents are involved in the transmission of a number of diseases to animals and humans, in particular Lyme borreliosis, tick-borne encephalitis, anaplasmosis and babesiosis. The aim of this research was to investigate the prevalence of Babesia spp., Borrelia burgdorferi s. l., Rickettsia spp., Anaplasma phagocytophilum in small rodents. A total of 118 rodents captured in the Curonian Spit were investigated. The captured rodents were identified as Apodemus flavicollis., Myodes glareolus, Microtus arvalis and Micromys minutus. For pathogens identification were used PCR, multiplex and nested PCR with genus and species specific primers. Results of analysis showed that rodents were infected with Babesia spp. and Anaplasma phagocytophilum.