Aiming reliable detection and localization of cerebral blood flow and emboli, embolic signals were added to simulated middle cerebral artery Doppler signals and analysed. Short-time Fourier transform (STFT) and continuous wavelet transform (CWT) were used in the evaluation. The following parameters were used in this study: the powers of the embolic signals added were 5, 6, 6.5, 7, 7.5, 8 and 9 dB; the mother wavelets for CWT analysis were Morlet, Mexican hat, Meyer, Gaussian (order 4) and Daubechies (orders 4 and 8); and the thresholds for detection (equated in terms of false positive, false negative and sensitivity) were 2 and 3.5 dB for the CWT and STFT, respectively. The results indicate that although the STFT allows accurately detecting emboli, better time localization can be achieved with the CWT. Among the CWT, the current best overall results were obtained with Mexican Hat mother wavelet, with optimal results for sensitivity (100% detection rate) for nearly all emboli power values studied.