The coherence method (COH) has been widely used to study the concordance between continuously measured signals intervening in the assessment of cerebral autoregulation in neonates. Several research groups have applied this method to mean arterial blood pressure (MABP) combined with cerebral signals such as the intravascular oxygenation (HbD), cerebral tissue oxygenation (TOI), and regional oxygen saturation (rSO(2)) measured by near-infrared spectroscopy (NIRS). All groups contributed in a particular way to the fine-tuning of the application of COH with the Welch averaged periodogram (WAP) method. We have made a comparative study of all published results coupled with an optimization of the use of the WAP method within COH. We have also proposed a pre-processing algorithm to remove signal artefacts, and defined a new critical score value (CSV) for COH to distinguish infants with impaired autoregulation from those without.