An electroporation apparatus provides for the electroporation of adherent cells attached to an electrode surface or suspended cells in close proximity to an electrode surface. In one embodiment, the electrodes are transparent to allow cell viewing using a microscope or an automated image analysis machine. The geometry of the electrodes and associated electrically non-conductive structures may provide for well-defined regions of electroporated and non-electroporated adherent cells with a clearly defined interface between these regions, facilitating comparison of electroporated cells and non-electroporated cells, and evaluation of transfer of material from cell to cell via intercellular gap junctions.