An integrated system for acquisition and processing of intracranial and extracranial Doppler signals and automatic embolic signal detection has been developed. The hardware basis of the system is a purpose-built acquisition/processing board that includes a multigate Doppler unit controlled through a computer. The signal-processing engine of the system contains a fast Fourier transform (FFT)-based, spectral-analysis unit and an embolic signal-detection unit using expert system reasoning theory. The system is designed so that up to four receive gates from a single transducer can be used to provide useful reasoning information to the embolic signal-detection unit. Alternatively, two transducers can be used simultaneously, either for bilateral transcranial Doppler (TCD) investigations or for simultaneous intra- and extracranial investigation of different arteries. The structure of the software will allow the future implementation of embolus detection algorithms that use the information from all four channels when a single transducer is used, or of independent embolus detection in two sets of two channels when two transducers are used. The user-friendly system has been tested in-vitro, and it has demonstrated a 93.6% sensitivity for micro-embolic signal (MES) identification. Preliminary in-vivo results also are encouraging.