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Threshold voltage variation due to quantum confinement effect in ultra-thin body silicon-on-insulator (SOI) MOSFETs is examined. It is experimentally demonstrated that threshold voltage variation drastically increases when SOI layer is thinned down to 3 nm. A percolation model is used to estimate the contribution of surface roughness to Vth variation. The method to suppress the threshold voltage variation is also proposed, and around 15% reduction in threshold voltage variation is experimentally demonstrated by applying substrate bias. The reason of the suppression can be explained by quantum confinement effect induced by substrate bias.