Aortic manipulation releases embolic material, thereby enhancing the probability of adverse neurologic outcomes following coronary artery bypass grafting (CABG). We prospectively evaluated 59 patients undergoing CABG. Patients in the single (SC, n = 37) and multiple clamp (MC, n = 22) groups were comparable in relation to age and operative risk (p > 0.05). Neurocognitive evaluation consisted of the Auditory Verbal Learning Test (AVLT), Color Trails Test A, the Grooved Pegboard test and the Mini-Mental State Examination. Data acquisition was performed preoperatively, early postoperatively and at the 4-month follow-up. Intraoperative transcranial Doppler (TCD) monitoring was used to quantify the embolic load in relation to different aortic clamping strategies. Preoperative neurocognitive results were similar between the groups (p > 0.05). The incidence of postoperative delirium was greater in the MC group but this failed to reach statistical significance (23% vs 8%, p = 0.14). SC patients had fewer embolization signals (270 ± 181 vs 465 ± 160, p < 0.0001). Early postoperative neurocognitive results were depressed in comparison to preoperative values in both groups (p < 0.05 for multiple comparisons). The magnitude of this cognitive depression was greater in the MC group (p < 0.05 for multiple comparisons). Preoperative levels of neurocognition were restored at follow-up in the SC group in all tests except the AVLT. A trend towards improvements in neurocognitive performances at follow-up was also observed in the MC group. Residual attention, motor skill and memory deficits were, however, documented with multiple tests. In conclusion, the embolic burden was significantly lower in the SC group. This TCD imaging outcome translated into fewer early cognition deficits and superior late restoration of function.