Background: Nowadays, Ehrlichia canis receives more attention because of its great morbidity and mortality in animals. Dogs in the subclinical and chronic phases can be asymptomatic, and serologic tests show cross-reactivity and fail to differentiate between current and past infections. Moreover, there could be low parasitaemia, and E. canis might be found only in target organs, hence negative by PCR in blood. Methods: We evaluated by PCR the prevalence of E. canis in blood, liver, spleen, lymphatic nodules, and bone marrow in 59 recently euthanized dogs that had ticks but were clinically healthy. Results: In total, 52.55% of the blood PCRs for E. canis were negative, yet 61.30% yield positive results in tissue biopsies as follows: 63.15% from bone marrow, 52.63% from liver, 47.36% from spleen and 15.78% from lymphatic nodules. In addition, 33% had infection in three tissues (spleen, liver and bone marrow). Conclusions: Our results show prevalence of E. canis in tissue from dogs that were negative by PCR in blood. E. canis DNA in tissue was 30% lower in dogs that tested negative in blood samples by PCR, compared to those that were positive. However, it must be taken into account that some dogs with negative results were positive for E. canis in others tissues.