In this article, the clinical experience with a cardiopulmonary bypass (CPB) using a newly developed hollow fiber oxygenator with an ultra-thin layer of silicone is reported. A comparative study of biocompatibility between the new oxygenator and a heparin coated oxygenator is also described. The CPB was performed with a silicone coated oxygenator, Mera Excelung Binding Prim HPO 15 H-C (Group I, n = 6) or Binding Prim HPO 25 H-C (Group II, n = 10) (Senko Medical Instrument Mfg., Tokyo, Japan). Air could be vented through the silicone coated hollow fibers, and it was easy to prime the circuits. The CPB duration was 101 +/- 37 min and 170 +/- 64 min for Groups I and II, respectively. There were no deaths and no complications from CPB. Partial arterial pressure of O2 levels 60 minutes after the start of CPB were 529 +/- 28 mm Hg and 529 +/- 28 mmHg for Group I and II, respectively. Partial arterial pressure of CO2 levels 60 min after the start of CPB were 36.4 +/- 4.6 mmHg and 39.4 +/- 4.4 mmHg, respectively. Plasma free hemoglobin at 60 min was 33.5 +/- 17.2 mg/ dL and 46.7 +/- 26.1 mg/dL for Groups I and II, respectively. As an evaluation of biocompatibility, the effects of the new oxygenator on platelet activation (GP Ib, IIb/IIIa), coagulation (TAT), fibrinolysis (PIC), and inflammatory response (C3a, granulocyte elastase) were investigated during CPB and comparing to those of the heparin coated oxygenator. There were no significant differences in GP Ib, GP IIb/IIa, TAT, PIC, and granulocyte elastase between the two oxygenators. However, 60 min after the start of CPB, the C3a was significantly lower for the new oxygenator group than for the heparin coated oxygenator group (p < 0.03). The new oxygenator showed good gas transfer, low hemolysis, and good biocompatibility. Because of its durability and good biocompatibility, the new oxygenator was determined to be suitable for prolonged extra corporeal circulation.