Background and Purpose: The clinical and epidemiologic features of Kawasaki disease (KD) suggest an infectious etiology; however, the agent(s) remain unknown. Our purpose was to isolate the causative bacterial gene from peripheral blood LEUKOCYTES of patients with acute KD, by Universal polymerase chain reaction (UPCR), in Tehran Children's Medical Center.Materials and Methods: Universal polymerase chain reaction (UPCR) assay was used to amplify the bacterial16S ribosomal RNA gene (rDNA).Results: Forty three (28 boys and 15 girls) were diagnosed with acute Kawasaki disease included in this study. The median age at diagnosis was 3.5 years (range: 0.5 -9 years). Twenty Nine (29) cases had typical KD criteria and 14 patients had atypical KD at diagnosis. Two of the 43 KD patients were positive for the Universal PCR assay for 16S rRNA, prior to intravenous g-globulin therapy (IVGT), while all specimens were negative by conventional blood culture. In our study, there was fever in 100%, conjunctivitis in 62.7%, rash in 83.72%, oral mucosal changes in 76.74%, peripheral changes in 37.20%, and cervical lymphadenopathy in 39.53% cases.Conclusion: The 16S rDNA sequence was positive in 4.65% of acute KD patients; this data shows that an infectious KD agent is traced in peripheral LEUKOCYTES. The question remains as to what true frequency ofthe16S rDNA sequence in KD is.