Thrombofibrinous and gaseous brain microemboli are commonly observed during extracorporeal circulation in patients undergoing cardiac surgery. Recent studies showed a preference of microemboli to the left hemisphere. We hypothesized that placement of the aortic cannula tip within the aorta descendens rather than in the aorta ascendens as commonly used reduces the number of microemboli to the brain and also reduces the side preference. Of 60 patients undergoing elective coronary artery bypass grafting primarily randomized to either a short aortic cannula (aorta ascendens) or an elongated one (aorta descendens), 29 (16 and 13) patients had complete and technically perfect continuous intraoperative transcranial Doppler sonography with embolus detection bilaterally. The number of high-intensity transient signals (HITS) was 994 +/- 2118 (mean +/- SD) for the short cannula group and was significantly lower with the elongated cannula (223 +/- 208; p < 0.02). HITS counts per min also differed significantly in favour of the aorta descendens group (p < 0.02), but there was an overlap. Thus, elongated cannulas can reduce, but not prevent microembolism to the brain. The side-to-side ratio of microemboli revealed more events in the left hemisphere, but this was similar in both groups. This suggests that individual anatomic factors may be responsible for this hemodynamically-mediated effect.