Canine arthropod-borne infections are of major interest in small animal practice and have been widely investigated in Central and Western Europe. However, only limited epidemiological data are available from South-Eastern European countries, although diseases including babesiosis or dirofilariosis are widely recognised as important canine infections in these countries. A steadily increasing number of dogs imported from South-Eastern Europe into Germany require particular attention by small animal practitioners. In this study, a total of 216 dogs [29 local Romanian pet dogs presented at Salvavet Veterinary Clinic in Bucharest, Romania, and 187 imported stray dogs from Romania (n = 109) and Hungary (n = 78) into Germany] were screened by molecular biological, serological and haematological methods for canine arthropod-borne infections. Eleven different parasitic and bacterial vector-borne pathogens-Babesia canis canis, Babesia canis vogeli, Babesia gibsoni, Babesia felis-like, Hepatozoon canis, Leishmania spp., Dirofilaria immitis, Dirofilaria repens, Acanthocheilonema reconditum, Anaplasma phagocytophilum and Mycoplasma haemocanis-were detected. Fifty-six percent of the dogs were positive by direct methods. B. canis canis was the most prevalent pathogen in dogs imported to Germany (42.8%) and dogs submitted for clinical consultation in Bucharest (44.8%). Our data strongly suggest the introduction of an adjusted screening panel in dogs from South-East Europe in view of increasing importation of dogs into Germany.