Microembolism generated during extracorporeal circulation is thought to be responsible for stroke and neuropsychological deficits. Before one can investigate the pathogenetic role in more detail, reproducible and reliable quantitative methods need to be developed. In several previous studies, microemboli detection was performed unilaterally. We questioned if this reflects the bihemispheric embolic load. In 42 patients undergoing coronary artery bypass grafting, bilateral embolus detection was performed during extracorporeal circulation. The side-to-side correlation of microembolus counts was strong (0.91), but there was a significant difference in number (p < 0.01) comparing left and right emboli. The side of higher embolus counts cannot be predicted in the individual because either side may show higher counts. Doubling the unilateral count may deviate from the bilateral count by as much as 51% in the individual patient. The total embolic load to the brain during extracorporeal circulation cannot be precisely predicted from unilateral transcranial insonation alone.