Cerebral autoregulation controls cerebral blood flow under changing cerebral perfusion pressure. Standards for measurement and analysis of dynamic cerebral autoregulation (dCA) are lacking. In this study, dCA reproducibility, quantified by intraclass correlation coefficient, is evaluated for different methodological approaches of transfer function analysis (TFA) and compared with multimodal pressure flow analysis (MMPF). dCA parameters were determined in 19 healthy volunteers during three 15-min lasting epochs of spontaneous breathing. Every spontaneous breathing epoch was followed by 5 min of paced breathing at 6 cycles/min. These six measurements were performed in both a morning and an afternoon session. Analysis compared raw data pre-processing by mean subtraction versus smoothness priors detrending. The estimation of spectral density was either performed by averaging of subsequent time windows or by smoothing the spectrum of the whole recording. No significant influence of pre-processing and spectral estimation on dCA parameters was found. Therefore, there seems to be no need to prescribe a specific signal-processing regime. Poor reproducibility of gain and phase was found for TFA as well as for MMPF. Based on reproducibility, no preference can be made for morning versus afternoon measurements, neither for spontaneous versus paced breathing. Finally, reproducibility results are not in favour of TFA or MMPF.Electronic supplementary materialThe online version of this article (doi:10.1007/s11517-010-0706-y) contains supplementary material, which is available to authorized users.