We studied perioperative renal damage in 22 patients with long-standing cyanotic congenital heart disease. Backround: Postoperative acute renal failure is a major complication of cardiac surgery associated with poor prognosis. Our study was designed to identify risk factors for renal failure in patients with cyanotic congenital heart disease. Patients: 22 cyanotic patients with a oxygen saturation of 82% (38–92%), age 14 years (5–42 years) and six controls with atrial septal defect, age 37 years (28–66 years) were investigated with repeated urinary analyses. Results: Before operation, six of 22 of the cyanotic patients had albuminuria. Postoperatively three patients developed acute renal failure including glomerular and tubular damage. Urinary albumin analysis >1000 mg g −1 creatinine after 24 h and N-acteyl-β- d-glucosaminidase analysis >100 U g −1 creatinine after 48 h predicted dialysis requirement. In noncyanotic controls only one preoperative and none of the postoperative analyses were pathological. Conclusions: Patients with cyanotic congenital heart disease are at risk for acute renal failure, which can be prognosed by urine analysis already 24 h after surgery. Cyanotic glomerulopathy should be known before surgery. To lower the risk, cardiopulmonary bypass time should be kept as short as possible and adequate hydration should be maintained in combination with extended diuretic therapy.