BackgroundCanine vector-borne diseases (CVBD) have become a major concern for canine and human public health. The aim of the study described here is to add epidemiological data regarding four pathogens responsible for CVBD, namely anaplasmosis, borreliosis, dirofilariosis and ehrlichiosis in a national survey conducted in Mexico.MethodsSeventy-four veterinary centres located in 21 federal Mexican states were asked to test dogs with clinical signs suspect for CVBD and healthy dogs, for detection of Dirofilaria immitis antigen and antibodies against Anaplasma spp., Borrelia burgdorferi (sensu lato) and Ehrlichia canis using the SNAP® 4DX® from IDEXX® Laboratories.ResultsA total of 1706 dogs were tested, including 943 apparently healthy and 722 CVBD-suspect dogs. Infected dogs were 36.7 %. The highest percentages of infection with E. canis (51.0 %) and Anaplasma spp. (16.4 %) were obtained in the northwestern region, while D. immitis was most frequently found in the northeastern region of the country (8.9 %). Four dogs from the northwestern, northeastern, eastern and southeastern regions, respectively, were positive for B. burgdorferi (sensu lato). Northcentral regions showed lowest overall prevalence of infection (2.4 %). Co-infections were detected in 8.8 % of the dogs tested. Statistically significant lower positivity was found among dogs aged less than one year (23.2 %) and small-sized dogs (27.6 %), while higher prevalence of infection was found in dogs living outdoors (42.0 %), dogs with detectable tick infestation (43.3 %) and dogs that received treatment for tick-transmitted infections (58.8 %). Seropositivity was a risk factor for the presence of clinical signs as follows: Anaplasma spp. (OR = 2.63; 95 % CI: 1.88–3.67; P < 0.0001), D. immitis (OR = 2.52; 95 % CI: 1.61–3.95; P < 0.0001), E. canis (OR = 3.58; 95 % CI: 2.88–4.45; P < 0.0001), mixed infections (OR = 4.08; 95 % CI: 2.79–5.96; P < 0.0001), one or more agents (OR = 3.58; 95 % CI: 2.91–4.42; P < 0.0001).ConclusionsCanine serological evidence supports that dogs from Mexico are at risk of acquiring Anaplasma spp., D. immitis and/or E. canis, while B. burgdorferi (sensu lato) transmission is minimal in the country. Practitioners play a fundamental role in the detection and control of these diseases to protect dogs and humans.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-016-1686-z) contains supplementary material, which is available to authorized users.