Background: The characteristics of the renal marker cystatin C (Cys-C) in association with the postoperative management of children with congenital heart disease (CHD) remain unclear. Methods and Results: Serum Cys-C and creatinine (Cr) levels were measured preoperatively and on the third postoperative day in 53 consecutive CHD patients (age, 1 day–11 years). On the third postoperative day, the patients were divided into 2 groups: the clinically severe group, requiring continuous infusion of diuretic drugs or peritoneal dialysis; and the non-severe group, composed of those without such needs. Preoperative Cys-C level decreased with age (by month) during the first year of life and remained almost constant thereafter, while Cr level increased with age. The Cys-C ratio (Cys-C level on the third postoperative day/preoperative level) was positively correlated with Cr ratio (R=0.57, P<0.001). Both Cys-C and Cr levels increased in correlation with the clinical severity of renal impairment. Receiver operating characteristic curve analysis failed to demonstrate an advantage of Cys-C over Cr in detecting severity. Conclusions: Cys-C may be a useful marker of renal function in terms of hemodynamic status in the postoperative management of CHD, although its superiority over Cr could not be confirmed. Future studies should clarify the role of Cys-C in clinical decision-making and evaluate the relationship of Cys-C with factors that may affect its levels.  (Circ J 2013; 77: 667–672)