The aim of this study was to compare different polymerase chain reaction (PCR) methods for the detection of Ehrlichia canis in blood samples and to relate these results to clinical findings and serology to E. canis using the indirect fluorescent antibody (IFA) test. Nine seropositive and nine seronegative dogs were included in this study. DNA was extracted once and used in one simple PCR and five nested PCR protocols previously described. In selected dogs (three seropositive and one seronegative) blood samples were aseptically collected in order to attempt the isolation of E. canis in the DH82 cell line. Results show that nested PCR protocols seem to be more sensitive than the simple PCR. Considering only nested PCR protocols, 33% of the IFA-positive samples were PCR positive using the five different protocols. The rest of the IFA-positive samples were PCR positive or negative depending on the protocol used. Clinical signs and laboratory findings compatible with canine monocytic ehrlichiosis (CME) were found in 67% of dogs positive by the IFA test. All samples positive by both techniques (IFA test and PCR) were from dogs suffering from clinical CME. IFA-negative samples were PCR negative, except 22% that were PCR positive when using only one of the nested PCR protocols. Isolation of the agent was exclusively achieved in the only case in which the IFA test and all the PCR protocols were also positive.