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The mechanism of the VT variation difference between NMOS and PMOS is investigated. It is clarified that there is no correlation between VT and physical parameters such as gate length, gate width, gate oxide thickness, gate taper angle, sidewall width, channel strain, and gate poly-Si grain structure by integrated physical analysis (IPA). In IPA, the physical parameters of transistors with VT of -5sigma, median, and +5sigma are evaluated. It is also clarified that the variations of gate depletion and random charges at the gate oxide interface are not the dominant factors of VT variation, by electrical analyses using the Takeuchi plot. In these analyses, VT variations with varying process parameters are investigated. As a result of the analyses, only random channel dopant fluctuation (RDF) has a significant effect on VT variation. Since the simple RDF model alone cannot explain the VT variation difference between NMOS and PMOS, the channel boron clustering model is proposed as a possible mechanism of NMOS VT enhancement.