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In most cases of inflammatory central nervous system [CNS] diseases in dogs, infectious agents remain undetected. Immunopathological studies suggest that such antigens may trigger an autoimmune response [“hit-and-Run hypothesis”] in some patients. In order to define the role of vector-borne pathogens in the aetiology of steroid-responsive meningitis-arteritis [SRMA] or meningoencephalomyelitis of unknown aetiology [MUE], blood and cerebrospinal fluid [CSF] of dogs were analysed for such pathogens. 66 client-owned dogs were included in the prospective multicenter study over a two year period. They were classified into 3 groups: 1] trauma group: dogs with non-inflammatory CNS diseases [n=21], 2] dogs with MUE [n=22], 3] dogs with SRMA [n=23]. DNA of A. phagocytophilum was found in EDTA-blood of 4 dogs [SRMA group]. Serological and PCR analyses for E. canis were negative in blood and serum of all dogs. B. henselae DNA was detected in blood of 1 dog [SRMA group]. There were no significant differences between the 3 groups regarding the seroprevalence of Bartonella spp. [n=61] and B. burgdorferi sensu lato [n=61]. Neither antibodies against TBEV in serum nor DNA of vector-transmitted agents was found in CSF in any of the dogs. Pasteurellaceae spp. DNA was detected in 3 dogs of the trauma group, suggesting contamination. There was no correlation between the presence of E. canis or B. henselae DNA or elevated antibody titers against E. canis, Bartonella spp., TBEV or B. burgdorferi sensu lato and inflammatory CNS diseases. A. phagocytophilum may play a role as a trigger of a secondary immunopathy.