There is limited information regarding the prevalence of many vector borne pathogens in Europe and especially in Spanish dogs. We investigated 206 sick and 260 clinically healthy dogs from three different regions in northeastern Spain for antibodies to Rickettsia conorii (Rc), Ehrlichia canis (Ec), Anaplasma phagocytophilum (Ap), Bartonella henselae (Bh), Bartonella vinsonii subsp. berkhoffii (Bvb), Leishmania infantum (Li) and Borrelia burgdorferi (Bb) and for antigen of Dirofilaria immitis (Di). Total prevalences were the following: Rc (56.4%), Li (30%), Ec (16.7%), Bh (16.8%), Ap (11.5%), Bvb (1.07%), Di (0.6%) and Bb (0.6%). Seroprevalences for Rc, Ec, Ap, Bh, and Bvb and Bb and Di antigens were similar among the three different study sites. The Ec seroprevalence, as determined by Snap 3DX, was statistically lower in dogs from Mallorca (0%) than Tarragona (16%) and Barcelona (5%) (P < 0.0001). Detection of Rc antibodies was associated with seroreactivity to Ec and Ap antigens (P = 0.018 and P = 0.002, respectively). IFA Ec antibodies were associated with Ap seroreactivity (P < 0.0001). There was no association between the clinical status, sex, time of the year when samples were collected, life-style or exposure to fleas or ticks and a positive test result for Ec, Bh, Bvb, or Bb antibodies or Di antigens. Li seroreactivity was associated with illness and living outdoors (P < 0.0001, P = 0.029; respectively), Rc seroreactivity with the male gender (P = 0.028) and Ap seroreactivity with living outdoors (P = 0.045). This study indicates that exposure to Rc, Li, Ec or related Ehrlichia spp., Bh and Ap or a related spp., is common whereas Di, Bb and Bvb is uncommon among dogs from the Mediterranean basin. We also provide serological data that suggests the existence of a novel Ehrlichia species on Mallorca island.