Because of many benefits from raw seed sprouts, consumers have consumed them largely. However, despite of many benefits, raw sprouts has been implicated in food-borne diseases. The source of food-borne disease related to raw seed sprouts is thought to originate from seeds contaminated by pathogenic bacteria. So, Intense Pulsed Light (IPL), a non-thermal processing method, is an effective device for seeds to maintain microbial safety without loss of seed viability. The objective of this research was to determine the effects on microbial inactivation and quality in radish and wheat seed by IPL treatment and to figure out the correlation between inactivation of seeds and surface roughness value (Ra). At 5th day of germination, the average germination rate and shoot length of radish sprouts by IPL at total fluences of 121 J/cm2 were 95% and 5.8 cm. It was not significant compared to the control group. And log reductions of radish and wheat seeds by IPL showed 1.0 and 1.2, respectively. The results showed radish seeds have higher tolerance to IPL treatment than wheat seed. Also, radish seed had the rougher surface (Ra=2.85 μm) than wheat seed (Ra=0.55 μm). Therefore, IPL can decontaminate microbial population on seeds, but the effectiveness of IPL is dependent on the surface morphology of seeds.