Autoregulation is an important feature of the cerebral circulation and it is affected in many diseases. Since during the last decades genetically modified mice turned to a fundamental tool in biomedical research a reliable technique for measuring cerebral autoregulation in mice is mandatory. However, this is possible only in anesthesia that unfortunately itself has a significant impact on cerebral perfusion and consequently might distort the measurements of cerebral autoregulation. At present, the literature on autoregulation in mice is quite small and consequently not very helpful in choosing an anesthetic protocol with lowest influence on cerebral vessels and high reproducibility for the measurement of cerebral autoregulation. In addition, simply transferring anesthetic protocols established in rats might not result in the same performance in mice. In the present study we systematically analyzed different common anesthetic protocols used in rodents on their effect on the measurement of cerebral autoregulation in mice using Laser Doppler Imaging. In spontaneously breathing mice we show that Halothane, Isoflurane and Pentobarbital abrogate autoregulation and that Ketamin/Xylazine as well as Chloralose have a moderate reproducibility. In contrast, Ethomidate has an excellent reproducibility although with this anesthesia the lower limit of cerebral autoregulation was lower than with Ketamin/Xylazine and Chloralose and that reported in the handful of papers (using Ketamin/Xylazine or Chloralose) so far dealing with this issue in mice. In spite of this we recommend Ethomidate for the measurement of cerebral autoregulation in mice because of its outstanding reproducibility.