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In this paper, we study the effect of phonon scattering in silicon nanowire field effect transistors (NWFET) using a Non-equilibrium Green’s function formalism in the effective mass approximation. The effect of electron-phonon scattering on the current voltage characteristics at high and low drain bias is investigated in detail. A wide range of cross-sections (from 2.2 × 2.2 to 6.2 × 6.2 nm2) and channel lengths (from 6 to 40 nm) are considered. The impact of phonon scattering on the electron current in different regions of the device characteristics is studied. Simulations including scattering in the whole transistor are compared with corresponding simulations in which scattering is only in the channel. Phonon limited mobility dependence on the NWFET cross-section and channel length is studied. The ballisticity coefficient, as a function of the channel length and gate voltage, is also computed for various channel cross-sections and lengths at high drain bias. The paper demonstrates that tunneling plays an important role in understanding the effect of phonon scattering at short channel lengths.