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In this paper the effect of microorganism size and shape on the killing efficiency of pulsed electric field (PEF) is investigated both experimentally and using a transient finite element program. The effect of cell size, membrane thickness, cell shape (spherical, elliptical, and cylindrical) on the calculated transmembrane voltage is studied. It has been found that both the cell size and cell membrane thickness have significant effect on the induced field across the cell membrane. The findings of the simulation results have been evaluated by comparing the trends with some experimental results. Five different types of microorganisms that have different shapes and dimensions have been inoculated with water at a conductivity level of 100 μS/cm and have been treated with the application of a pulsed electric field of 70 kV/cm. Significant difference in bacteria reduction was noticed between the treated cells which could be attributed to the cell size and shape.