Background: Ehrlichia canis is a tick-borne bacterium that causes severe, life-threatening disease in dogs, being more prevalent in tropical and subtropical countries. Randomized studies conducted in Brazil indicate that the prevalence of E. canis infection in dogs ranges from 0.7% to over 50.0%. In a study conducted in northern Brazil, the prevalence was higher in dogs from urban areas, as compared to dogs from rural areas. In the present study, we investigated the exposure to Ehrlichia spp. infection in dogs from remote indigenous villages located in a rural area in north-eastern Brazil. Methods: From March to June 2015, 300 privately owned dogs were blood sampled and tested by a rapid ELISA and by a conventional PCR in order to detect anti-Ehrlichia spp. antibodies and E. canis DNA, respectively. Additionally, dogs were also tested for anti-Anaplasma spp. antibodies and Anaplasma platys DNA, using the same diagnostic approaches. Positivity was correlated with tick infestation and dogs’ data (gender, age and level of restriction). Results: Overall, 212 (70.7%) dogs were positive for at least one test targeting Ehrlichia spp. In particular, 173 (57.7%) dogs were positive only by rapid ELISA, 5 (1.7%) only by PCR and 34 (11.4%) were simultaneously positive by both tests. In the same way, 39 (13.0%) dogs presented detectable E. canis DNA in their blood, whereas 18 (6.0%) dogs were A. platys DNApositive. Coupling serological and PCR data, 63 (21.0%) dogs were simultaneously positive to Ehrlichia spp. and Anaplasma spp. Positivity rates for both Ehrlichia spp. and Anaplasma spp. were higher among dogs more than 1 year of age. Sick dogs were more positive to Ehrlichia spp. as compared to healthy dogs. Conclusions: Dogs from rural areas in north-eastern Brazil are highly exposed to Ehrlichia spp. infection and positivity rates do not necessarily correlate with current tick infestation load, since only one infected tick bite is needed to get the infection. This reinforces the importance of keeping dogs free of ticks, in order to reduce as much as possible the risk of infection by E. canis and other tick-borne pathogens such as Babesia vogeli, which are usually co-endemic.