Abstract: In this study, we present the microfabrication and characterization of a transparent microelectrode array (MEA) system based on PEDOT:PSS for electrophysiology. The influence of the PEDOT:PSS electrode dimensions on the impedance was investigated and the stability over time under physiological environment was demonstrated. A very good transparency value was obtained by our system displaying one of the best impedance and transmittance values when compared to other transparent MEA. After biocompatibility validation, we successfully recorded spontaneous neuronal activity of primary cortical neurons cultured over 4 weeks on the transparent PEDOT:PSS electrodes. This work shows that microelectrodes composed of PEDOT:PSS are very promising as a new tool for both electrophysiology and fluorescence microscopy studies on neuronal cell cultures.