Phase synchrony analysis is a relatively new concept that is being increasingly used on neurophysiological data obtained through different methodologies. It is currently believed that phase synchrony is an important signature of information binding between distant sites of the brain, especially during cognitive tasks. Electroencephalographic (EEG) recordings are the most widely used recording technique for recording brain signals and assessing phase synchrony patterns. In this study, we address the suitability of phase synchrony analysis in EEG recordings. Using geometrical arguments and numerical examples, employing EEG and magnetoencephalographic data, we show that the presence of a common reference signal in the case of EEG recordings results in a distortion of the synchrony values observed, in that the amplitudes of the signals influence the synchrony measured, and in general destroys the intended physical interpretation of phase synchrony.