The clinical signs of Ehrlichia canis and Anaplasma platys infection are similar, and the diagnosis of these pathogens made by stained blood smears is poor due sensibility and specificity. On the other hand, the molecular diagnosis is highly sensitive and specific and nested-PCR have been optimized for accurate diagnosis these pathogens in dogs. At the veterinary teaching hospital, whole-blood samples with EDTA were obtained from 100 dogs and smears were made from blood samples for evaluation for intracellular parasites. For each sample, DNA was extracted and submitted to nPCR analysis for detection of E. canis and A. platys. The results of stained blood smears showed 9% of the animals were positive for E. canis and 21% for A. platys. Regarding of nPCR analysis, 57 and 55% of dogs were positive for E. canis and A. platys respectively. As compared to a nested PCR, the stained blood smears revealed false-negative results for both E. canis and A. platys. The results indicate that the nPCR is highly sensitive and specific for detection of both pathogens and the molecular diagnosis could be more useful at veterinary hospital.