BACKGROUND: Infection with Ehrlichia canis, a gram negative obligatory intracellular bacterium, causes canine monocytic ehrlichiosis which is the worldwide disease in dogs. OBJECTIVES: The objective of this study was to investigate the prevalence of E. canis in thrombocytopenic dogs using nested PCR and diagnostic role of thrombocytopenia in the infection. METHODS: Blood samples collected from 40 dogs attended in Teaching small animal hospital of Tehran University were classified as group A (platelet counts below 101.000/µL, thrombocytopenic, n=11), B (101.000-200.000/µL, thrombocytopenic, n=15) and C (platelet counts more than 201.000/µL, non-thrombocytopenic, n=14) according to their platelet counts. 16S rRNA was analyzed by nested PCR using specific primers. RESULTS: 16S rRNA gene fragment of E. canis were detected in five samples of group A (45.5%), three samples of group B (20%), and one sample of group C (7.1%). Prevalence rate of infection was statistically higher in group A than the other groups (p=0.02). In total, approximately one third of thrombocytopenic dogs had demonstrable E. canis infection (30.7%). CONCLUSIONS: while thrombocytopenia cannot be considered as specific marker for detection of E. canis infection, it can be used as a surveillance test prior to other diagnostic methods.