High throughput system maximizes electroporation yields of mammalian, bacterial and yeast cell lines. Suited for the delivery of siRNA and DNA expression vectors into mammalian cells, the system provides a 96-well electroporation plate and a 96-well plate handler for the design of electroporation experiments and for efficient gene delivery. The interface allows variable voltage and pulse length, and 96 samples are processed in <1 min. The system is compatible with the Enhancer 3000 QC monitoring system, exponential decay generators and square wave generators.