Canine vector-borne diseases (CVBDs) pose a diagnostic challenge, particularly when a dog is coinfected with more than one pathogen. The purpose of this study was to generate information about the diagnosis of CVBDs in young dogs following their first exposure to flea, tick, sand fly, louse, and mosquito vectors. From March 2008 to May 2009, 10 purpose-bred young naive beagle dogs and a cohort of 48 mixed-breed dogs living in an area to which CVBD is endemic in southern Italy were monitored using different diagnostic tests (cytology, serology, and PCR). Overall, PCR detected the highest number of dogs infected with Anaplasma platys, Babesia vogeli, and Ehrlichia canis, whereas seroconversion was a more sensitive indicator of exposure to Leishmania infantum. For A. platys infection, combining blood and buffy coat cytology in parallel enhanced the relative sensitivity (SE(rel)) (87.3%). For B. vogeli, the best diagnostic combination was buffy coat cytology and serology used in parallel (SE(rel), 67.5%), whereas serology and PCR used in parallel (SE(rel), 100%) was the best combination for L. infantum. Overall, 12 (20.7%) dogs were coinfected; however, the percentage of new coinfections decreased from baseline (50%) to the first (33.3%) and second (16.6%) follow-up time points. Numbers of coinfections with A. platys and B. vogeli were significantly higher (P < 0.05) than coinfections with other pathogen combinations. The data generated in this study provide insights on the incidence of certain pathogens infecting young dogs in southern Italy, highlight important diagnostic testing limitations, and support the use of multiple diagnostic modalities when attempting to confirm a tick-borne infection in an individual dog or in a canine population.