We experienced a case of a 3-year-old boy who presented signs and symptoms of Kawasaki syndrome. Two blood culture sets were processed by the hospital microbiology laboratory using a standard blood culturing system. The anaerobic bottles gave a positive result at day 3 after inoculation. The biochemical profiles produced by the RapID ANA II System showed that the organism was Clostridium baratii with a probability of 99%. Our case highlights the importance of C. baratii as a potential human pathogen and reports the associations with manifestations, which, to our knowledge, have not been previously described concomitantly with a clostridial infection.