In this work, we present a simple technique for building interconnected 3-Dimensional (3D) neuronal networks coupled to Micro-Electrode Array (MEA) substrates. Particularly, we designed a confinement structure made of PDMS (poly-dimethyl-siloxane) for realizing two structurally and functionally interconnected 3D neuronal networks in vitro. The inter-population links are obtained by means of two groups of ten micro-channels with specific spacing and heights. This experimental model presents a real 3D architecture mimicking the in vivo condition and exhibiting spontaneous activity with structural and functional connections between the two compartments. We characterized the dynamics of these 3D interconnected assemblies in terms of spiking and bursting activity and we estimated the connectivity by means of a recently developed cross-correlation based algorithm. The obtained results suggest new avenues for the use of such an in vitro 3D model for studying brain (dys)function and for co-culturing neuronal cells towards the development of `organ-on-chip' microsystems.