Abstract: The present disclosure relates to a high throughput, scalable system for electroporation of biological cells. The two part system comprises an electroporation reaction array that interfaces with a control unit, providing electrical pulse, temperature control, and mixing of the sample contents. The control unit automates the entire process; electroporation, cell recovery and outgrowth are performed in a electroporation array assembly. The bottom of each reaction well of the electroporation array assembly contains a pair of coplanar electrodes. The bottom surface containing the electrodes is treated in a way to render it hydrophilic. This results in increased wetting of the electrodes thereby increasing transformation efficiency. The electrode configuration allows for processing of smaller sample volumes, reducing the consumption of expensive biological reagents by several orders of magnitude compared to conventional cuvette-based electroporation devices.