Background: Acute renal failure is an occasional complication after cardiopulmonary bypass in infants. Whereas it is well known that postoperative hemodynamics inflict acute renal failure, the influence of extra-corporeal circulation on the kidney is less clear. Moreover, changes in blood viscosity occur during and after surgery, which may influence renal dysfunction. For this reason, we investigated the impact of blood viscosity on renal function during cardiopulmonary bypass. Methods: In 34 patients weighting less than 10 kg, we performed repeated analysis of urine, blood, and plasma viscosity. Results: Polyuria and proteinuria that appeared during cardiopulmonary bypass indicated an elevated transglomerular filtration gradient, which recovered within 24 hours. The appearance of N-acetyl-β-D-glucosaminidase in the urine, and elevated excretion of sodium, were additionally indicative of mild tubular damage. Elevation of blood viscosity during hypothermic perfusion showed a statistical correlation with proteinuria and N-acetyl-β-D-glucosaminidaseuria. With hypothermia, the relation of blood viscosity to plasma viscosity became stronger, while the relation to the hematocrit decreased compared to normothermia. Conclusions: During cardiopulmonary bypass perfusion, the kidney can be stressed by proteinuria and mild tubular damage. Our data provide evidence that the kidneys can be protected by improved blood viscosity during cardioplegia, but this needs confirmation in a prospective interventional study.