The objective of this open cohort study was to assess the association between neurological complications in patients with definite native-valve infective endocarditis (IE) and cerebral microembolism (MES). MES detection was performed with 1-h, bilateral middle cerebral arteries (MCA) insonation using a transcranial Doppler ultrasound (TCD) machine. Thirty patients with definite native-valve IE were stratified into 2 groups based upon the presence of MES. The most striking difference between the 2 groups of patients was the incidence of clinically evident neurological complications. Neurological complications of IE occurred in 10 (83.3%) patients with positive MES and in 6 (33.3%) MES-negative patients (p=0.021). Ischaemic stroke was the most common complication, occurring in 11 of 16 patients, followed by meningitis in 4 patients and cerebritis in 1 patient. There was a trend towards greater in-hospital mortality in patients with recorded MES than in the MES-negative, although this was not statistically significant (33.3% vs 16.6%; p=0.392). Our results reveal a significant association between MES and neurological complications in patients with native-valve IE. TCD is a promising tool in predicting individual patient risk for neurological complications of IE.