An electroporator for high-throughput electroporation is constructed with a well plate in which each well has internal electrodes that extend beyond the opening of the well to form contact areas, either as horizontal platforms extending laterally from the well rims or as extended heights of thin electrode plates. The electroporator also includes a lid that contains circuitry and electrical contacts that mate with the exposed contact areas in the well plate. The interchangeability of lids allows the wells to be shocked according to different protocols.