Ultrathin silicon-on-insulator (UTSOI) technology1 has emerged as a key candidate for sub-100nm gate length CMOS devices. Recent experiments have characterized MOSFETs with silicon channels as thin as 1nm (four atomic layers of silicon),2,3 and found them to be well-behaved electrically. Quantum effects are important to the electron transport in such devices, and the penetration of the electron wavefunction into the gate oxide introduces new scattering mechanisms. We introduce here a novel method for first-principles calculation of electron mobilities in ultrathin SOI channels, including surface roughness and defect scattering. The electronic structure and scattering potentials are calculated with Density Functional Theory in the Local Density Approximation (DFT-LDA), and the mobility is calculated through Green's functions. The method requires little computational effort beyond that of the DFT-LDA calculations, and allows the calculation of temperature- and carrier concentration-dependent mobilities. Since the silicon-oxide interface is treated at the atomic-scale, the mobility contributions of different defects (e.g. suboxide bonds, oxide protrusions) and impurities (e.g. nitrogen, hydrogen) can be calculated separately, giving a precise physical picture of channel electron transport.