Abstract Background Persistent fever after intravenous immunoglobulin (IVIG) is considered to be a major criterion of IVIG resistance in Kawasaki disease (KD), and a risk factor for the development of coronary artery abnormalities (CAA). However, the importance of persistent non-fever symptoms after defervescence has not yet been investigated. We examined the relationship between persistent non-fever symptoms and CAA in KD. Methods We conducted a retrospective cohort study of patients hospitalized with KD at the National Center for Child Health and Development between 1 April 2008 and 31 March 2009. Patients were divided into two groups; group A included patients who still had non-fever symptoms one month after onset of the illness and group B included patients who did not have persistent non-fever symptoms. Demographic, clinical variables were compared between the groups. Results Seventy-seven KD patients treated with IVIG were retrospectively analyzed. Patients were divided into two groups; group A included 12 (15.6%) patients and group B 65 (84.4%) patients. Demographic data, baseline laboratory data, and fever duration did not differ between the groups. In group A patients the most common persistent non-fever symptoms were lip erythema (n = 6) and bulbar conjunctivitis (n = 8). One month after onset of the illness CAA developed in seven of 77 patients (9.1%), four (33%) in group A and three (4.6%) in group B (odds ratio 10.3; 95% CI 1.9-54.8). Three patients in group A and one patient in group B developed CAA after the resolution of fever. Conclusions Persistence of non-fever symptoms after IVIG may suggest persistence of latent inflammation, which may increase the risk of CAA. Therefore, patients with persistent non-fever symptoms may be at risk of developing CAA, even after defervescence. A prospective trial of additional IVIG for such patients should be considered.