Microemboli generated during extracorporeal circulation (ECC) are likely to induce neurological sequelae. This study examines whether the choice of a distinct type of ECC can reduce intracerebral emboli counts. Middle cerebral artery blood flow during coronary artery bypass grafting was monitored continuously by transcranial Doppler ultrasound in 45 patients. The ECC systems used were a roller pump (n = 16), a centrifugal pump (n = 18) and a combination of centrifugal pump and heparin-coated ECC system (n = 11). Patients’ characteristics as well as surgical and anesthesiological procedure did not differ between the groups. Total counts did not differ significantly between the three groups. Intraoperative events in individual patients may lead to massive embolus generation overcoming positive properties of a distinct ECC system.