Canine monocytic ehrlichiosis (CME) is a tick-borne disease of dogs caused by the rickettsia Ehrlichia canis, which has a worldwide distribution. The aim of this study was to identify molecular alterations in patients with natural infection with E. canis before and after treatment with doxycycline. Fifty different breeds, gender and ages of canine patients which were diagnosed positive to E. canis by a commercial ELISA test (IDEXX®), and showed clinical signs compatible with CME at the time of the test were included. In all cases, a blood sample was taken before and after treatment with doxycycline for PCR diagnosis of E. canis. Before treatment, of the fifty ELISA-positive dogs, only seven were positive for E. canis in PCR analysis. After treatment, ten dogs were positive to E. canis by PCR, of which only four were also positive before treatment. Of the seven positive dogs before treatment, four of them remained positive after treatment, and only three obtained a negative result post treatment. Notably, six dogs with negative results prior to treatment with doxycycline tested positive after treatment ended. This may be due mainly to two reasons: first, that the rickettsemia was not high enough to be detected by PCR or, that during treatment with doxycycline there was no control of the vector tick of E. canis. In conclusion, probably E. canis has a natural resistance to doxycycline and such others authors mentioned, in CME possibly the rickettsias are in reservoir organs such as spleen.