Described are electroporation plates (2) that comprise a plurality of energizable electroporation wells (4) or chambers arrayed in a solid substrate, wherein at least two of the wells (4) in the plate (2) can be independently energized. Each well (4) contains at least two electroporation electrodes (12, 14) disposed therein, and serves as the vessel in which an individual electroporation reaction can be conducted. Also, described are electroporation systems that use electroporation plates (2) according to the invention, as well as methods of using such electroporation plates (2) and systems, for example, to optimize electroporation conditions.