Cerebral Autoregulation, in clinical practice, is assessed by means of correlation or coherence analysis between mean arterial blood pressure (MABP) and cerebral blood flow (CBF). However, even though there is evidence linking cerebral autoregulation assessment with clinical outcome in preterm infants, available methods lack precision for clinical use. Classical methods, used for cerebral autoregulation, are influenced by the choice of parameters such as the length of the epoch under analysis and the choice of suitable frequency bands. The influence of these parameters, in the derived measurements for cerebral autoregulation, has not yet been evaluated. In this study, cerebral autoregulation was assessed using correlation, coherence, a modified version of coherence and transfer function gain, and phase. The influence of the extra-parameters on the final scores was evaluated by means of sensitivity analysis. The methods were applied to a database of 18 neonates with measurements of MABP and tissue oxygenation index (TOI). TOI reflects changes in CBF and was measured by means of near-infrared spectroscopy.