Introduction: The aim of this prospective study was to determine the frequency and composition of cerebral microemboli in a paediatric population during transcatheter atrial septal defect closure. Methods: Multi-frequency transcranial Doppler was used to detect microembolic signals in the middle cerebral artery of 24 patients. Embolic signals were automatically identified and differentiated according to their composition, gaseous or solid. The procedure was divided into five periods: right cardiac catheterisation; left cardiac catheterisation; pulmonary angiography; balloon sizing; and device placement. Results: Microemboli were detected in all patients. The median number of signals was 63 and over 95% gaseous. The total number of microembolic signals detected during two periods – balloon sizing and sheath placement and device placement – was not significantly different (median: 18 and 25, respectively) but was significantly higher than each of the other three periods (p<0.001). In eight patients, the device was opened more than once and the number of embolic signals decreased with each successive device deployment. There was no correlation between the number of microembolic signals and fluoroscopic time, duration of procedure, age, or device size. Conclusion: This is the first study to investigate the timing and composition of cerebral microemboli in a paediatric population during cardiac catheterisation. Microembolic signals were related to specific catheter manipulations but were not associated with fluoroscopic time or duration of procedure.