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This paper presents a new, 3-D Monte Carlo approach for modeling random dopant fluctuation effects in MOSFETs. The method takes every silicon atom in the device into account and is generally applicable to arbitrary nonuniform doping profiles. In addition to body dopant fluctuations, the effect of source-drain dopant fluctuations on short-channel threshold voltage is studied for the first time. The result clearly indicates the benefit of retrograde body doping and shallow/abrupt source-drain junctions. It also quantifies the magnitude of threshold voltage variations due to discrete dopant fluctuations in an optimally designed 25 nm MOSFET.