Recently several cases of theileriosis due to the haemoprotozoan Theileria buffeli/orientalis have been recorded in the Apulian region, Italy. In this area other tick-borne pathogens were usually identified such as Anaplasma marginale and Babesia bigemina. Outbreaks were recorded showing that these pathogens can be observed separately or in mixed infections. Sub-clinical cases and carrier animals were also previously identified. A lack of specific techniques could not rule out the presence of other haemoparasites such as T. annulata, B. divergens, B. bovis, Ehrlichia phagocytophila and E. bovis. Moreover little is known about the tick species involved in the dissemination of these diseases. Therefore more powerful techniques to specifically identify Theileria or Babesia species have been recently developed. A PCR technique and reverse line blotting (RLB) system to specifically identify six Theileria species and three Babesia species were used. T. buffeli/orientalis and B. bigemina were the only pathogens observed in the targeted animals. The authors also present some changes in blood parameters for the animals followed during this study.