We investigated the co-occurrence of the nine of the most relevant canine vector-borne pathogens (CVBP) using conventional and real-time PCR and evaluated risk factors and potential non-apparent haematological alterations associated with co-infection in 111 rural, owned, free-ranging dogs in the Metropolitan Region of Chile.At least one pathogen was detected in 75% of the dogs. DNA ofAnaplasma platys(Ap; 36%),CandidatusMycoplasma haematoparvum (CMhp; 31%),Mycoplasma haemocanis(Mhc; 28%),Trypanosoma cruzi(17%),Leishmaniaspp. (4.5%), andAcanthocheilonema reconditum(1%) was detected. All dogs were negative forEhrlichiaspp.,Rickettsiaspp.,Bartonellaspp., Piroplasmida, andHepatozoonspp. Thirty-eight dogs (34%) were coinfected. CMhp was involved in 71%, Mhc in 58%, and Ap in 50% of the co-infections. The most common co-infection pattern was CMhp–Mhc (37% of the cases). The prevalence of Ap was higher in juvenile than in adult dogs, whereas the opposite was found for CMhp and Mhc. Adult dogs were four times more likely of being co-infected than juveniles. Co-infected animals showed higher white blood cell count, segmented neutrophil count, and GGT levels than non-co-infected dogs. Clinically healthy but infected dogs may act as reservoirs of CVBP, and their free-ranging behavior would facilitate the spread of these pathogens to other dogs as well as human beings or wild carnivores.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11259-022-10009-6.