Electrotransfection has been widely used as a versatile, non-viral method for gene delivery. However, electrotransfection efficiency (eTE) is still low and unstable, compared to viral methods. To understand potential mechanisms of the unstable eTE, we investigated effects of electrode materials on eTE and viability of mammalian cells. Data from the study showed that commonly used metal electrodes generated a significant amount of particles during application of pulsed electric field, which could cause precipitation of plasmid DNA from solutions, thereby reducing eTE. For aluminum electrodes, the particles were composed of aluminum hydroxide and/or aluminum oxide, and their median sizes were 300 to 400 nm after the buffer being pulsed 4 to 8 times at 400 V cm-1, 5 ms duration and 1 Hz frequency. The precipitation could be prevented by using carbon (graphite) electrodes in electrotransfection experiments. The use of carbon electrodes also increased cell viability. Taken together, the study suggested that electrodes made of inner materials were desirable for electrotransfection of cells in vitro.