This study evaluated the diagnosis of atypical Kawasaki disease (KD) in accordance with the new American Heart Association (AHA) criteria. Diagnosis and treatment of this disease is always delayed in patients with prolonged fever and suspected KD, because they do not completely satisfy the traditional AHA criteria for KD. We report the cases of two patients with atypical KD. KD was successfully diagnosed in both patients by using the new AHA diagnostic algorithm, and a good response to the initial treatment with intravenous immunoglobulin was observed within 10 days of KD onset. Herein, we report these cases and review the literature.