Blood samples were collected from 100 shepherd dogs, 12 hunting dogs and 14 stray dogs (apparently healthy) in southern Hungary to screen for the presence of emerging tick-borne pathogens. Based on real-time PCR results, 14 dogs (11%) had single or dual haemoplasma infection, and a same number of samples were positive for Anaplasma phagocytophilum. In one sample Coxiella burnetii was molecularly identified, and 20.3% of dogs seroconverted to the Q fever agent. Rickettsaemia (sensu stricto) was also detected in one animal. This is the first molecular evidence of autochthonous infection of dogs with the above pathogens in Hungary. The relatively high prevalence of haemoplasma and anaplasma infection among non-pet dogs is suggestive of a prolonged carrier status and bacteraemia of these animals rendering them epidemiologically significant as potential reservoirs and sentinels for tick-borne infections.