Objective: Exposure to cerebral emboli is ubiquitous and may be harmful in cardiac surgery utilizing cardiopulmonary bypass. This was a prospective observational study aiming to compare emboli exposure in closed-chamber with open-chamber cardiac surgery, distinguish particulate from gaseous emboli and examine cerebral laterality in distribution. Methods: Forty patients underwent either closed-chamber procedures ( n = 20) or open-chamber procedures ( n = 20). Emboli (gaseous and solid) were detected using transcranial Doppler in both middle cerebral arteries in two monitoring phases: 1, initiation of bypass to the removal of the aortic cross-clamp; and 2, removal of aortic cross-clamp to 20 minutes after venous decannulation. Results: Total (median (interquartile range)) emboli counts (both phases) were 898 (499–1366) and 2617 (1007–5847) in closed-chamber and open-chamber surgeries, respectively. The vast majority were gaseous; median 794 (closed-chamber surgery) and 2240 (open-chamber surgery). When normalized for duration, there was no difference between emboli exposures in closed-chamber and open-chamber surgery in phase 1: 6.8 (3.6–15.2) versus 6.4 (2.0–18.1) emboli per minute, respectively. In phase 2, closed-chamber surgery cases were exposed to markedly fewer emboli than open-chamber surgery cases: 9.6 (5.1–14.9) versus 43.3 (19.7–60.3) emboli per minute, respectively. More emboli (total) passed into the right cerebral circulation: 985 (397–2422) right versus 376 (198–769) left. Conclusions: Patients undergoing open-chamber surgery are exposed to considerably higher numbers of cerebral arterial emboli after removal of the aortic cross-clamp than those undergoing closed-chamber surgery, and more emboli enter the right middle cerebral artery than the left. These results may help inform the evaluation of the pathophysiological impact of emboli exposure.