Aims: Kawasaki disease is an acute pediatric vasculitis whose etiology remains unknown but epidemiology and clinical presentation suggest a viral etiology. We performed unbiased high-throughput-sequencing on blood of patients with Kawasaki Disease (KD). Materials and Methods: High-throughput-sequencing was performed directly on blood of children with typical KD. Sequences were aligned against a database of clinically relevant viruses. Results: Four patients were acutely infected in the blood, with respectively, poliovirus (vaccine strain), measles (vaccine strain), rhinovirus and bocavirus. Patients with poliovirus and measles had received oral polio and measles vaccines, respectively, twelve and 2 weeks prior. Conclusion: Viral signatures were identified in more than half of the patients, including some corresponding to their vaccinal history. This could suggest a temporal association with KD.