Elevation of tissue-destructive proteases has been reported in acute Kawasaki disease. Cystatin C is a naturally occurring inhibitor of elastolytic cysteine protease in humans. Serum cystatin C deficiency in human beings has been linked to atherosclerosis and aortic aneurysms. We investigated the serum levels of cystatin C during acute Kawasaki disease. Serum samples from 17 acute Kawasaki disease patients were collected before and after immunoglobulin therapy and also at a median of 17 days after the therapy. Eight adults and 10 children without intercurrent infections served as control patients. Children with Kawasaki disease prior to therapy had significantly lower levels of cystatin C compared to adults (p = 0.002) and control children (p = 0.001). The low levels persisted 1–106 days after the therapy. Compared to control children and adults, children with Kawasaki disease had significantly lower serum levels of cystatin C in the acute stage before immunoglobulin therapy and in the subacute phase after the immunoglobulin therapy.