To assess renal inflammation and its sequelae in Kawasaki disease (KD) patients, we conducted a prospective study in a university medical center setting in Taiwan. From June 2002 to January 2005, 50 children with KD were enrolled, and after admission, all received technetium-99m dimercaptosuccinic acid scintigraphy single photon emission computed tomography (DMSA renal SPECT), the results of which were used as the reference standard for determining renal inflammation. Patients with renal inflammation underwent another DMSA renal SPECT more than 6 months later to evaluate the sequelae. We found that 26 of the 50 patients (52%) had renal inflammatory foci. There were no significant relationships between clinical or laboratory parameters and renal involvement in KD, except the presence of coronary artery lesions [P<0.01; odds ratio (OR) 5.18; 95% confidence interval (CI) 1.52-17.65]. Although all patients were free of clinical symptoms, the 6-month follow-up DMSA renal SPECT showed renal scarring in 11 of the 24 patients (46%). Patients with an initial abnormal renal ultrasound did predict a greatly increased risk of scarring (P<0.05; OR 16.2; 95% CI 1.27-206.20). In conclusion, this study demonstrated that the potential long-term clinical impact of KD is not limited to coronary artery lesion sequelae but also includes renal scar formation.