Purpose: Respiratory symptoms are frequently observed in children with Kawasaki disease (KD) during the acute phase. The association rate of KD with antecedent respiratory illness has been reported to range from 56 to 83%. Clinical and epidemiologic features of KD support an infectious cause, but the etiology remains unknown. Patients with KD who harbor respiratory viruses more frequently show coronary artery dilatation and are more often diagnosed with incomplete presentation of the disease. Therefore, we investigated the association of respiratory viruses in children with KD using multiplex reverse transcriptase-polymerase chain reaction (RT-PCR). Methods: 114 KD patients were enrolled from January 2010 to June 2013. Two study groups (Group 1; n=94, KD without respiratory symptoms, Group 2; n=20, KD with respiratory symptoms) were compared with a control group (Group 3; n=49, febrile patients with respiratory symptoms). Laboratory data were obtained from each patient including complete blood count (CBC), erythrocyte sedimentation rate (ESR), platelet count, alanine aminotransferase (ALT), aspartate aminotransferase (AST), serum total protein, albumin, C-reactive protein (CRP), NT-pro brain natriuretic peptide (BNP). Echocardiographic measurements were compared between the three groups. RT-PCR was performed using nasopharyngeal secretion to screen for the presence of 14 viruses (corona virus, parainfluenza virus 1,2 and 3, influenza A and B, respiratory syncytial virus A and B, rhino virus A, B and C, metapneumo virus, adenovirus, and vocavirus) in groups 2 and 3. Results: The rate of KD with respiratory symptoms was 17.5%. The duration of fever was significantly longer and coronary artery diameter was significantly larger in group 2 than in group 1. Coronary artery diameter, CRP, platelet count, ALT, and NT-pro BNP were significantly higher and albumin lower in group 2 compared with group 3. Detection rate of adenovirus was 55.0% in group 2 and 28.6% in group 3. Conclusion: A positive RT-PCR for respiratory viruses may be helpful to elucidate the specific virus in KD patients with respiratory symptoms. NT-proBNP is a very important diagnostic tool in differentiating KD from other febrile viral respiratory infections.