Objective. In many applications, multielectrode arrays employed as neural implants require a high density and a high number of electrodes to precisely record and stimulate the activity of the nervous system while preserving the overall size of the array as little as possible. Approach. Here we present a multilayer and three-dimensional (3D) electrode array, together with its manufacturing method, enabling a higher electrode density and a more efficient signal transduction with the biological tissue. Main results. The 3D structure of the electrode array allows a multilayer placement of the interconnects within a flexible substrate, it narrows the probe size per the same number of electrodes, and it maintains the electrode contacts at the same level within the tissue. In addition, it augments the electrode surface area, leading to a lower electrochemical impedance and a higher charge storage capacity. To characterize the recordings capabilities of the multilayer 3D electrodes, we measured visually evoked cortical potentials in mice and analysed the evolution of the peak prominences and latencies according to different light intensities and recording depths within the brain. The resulting signal-to-noise ratio is improved compared to flat electrodes. Finally, the 3D electrodes have been imaged inside a clarified mouse brain using a light-sheet microscope to visualize their integrity within the tissue. Significance. The multilayer 3D electrodes have proved to be a valid technology to ensure tissue proximity and higher recording/stimulating efficiencies while enabling higher electrode density and reducing the probe size.