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Ultrathin AlN/GaN heterojunctions are highly attractive for high-frequency transistor applications. In this work, remote surface roughness (RSR) scattering mediated by the high polarization is studied as a new scattering mechanism in such structures. In both depletion-mode and enhancement-mode devices with ultrathin AlN barriers, RSR scattering can be of the same order as polar optical phonons, the dominant scattering mechanism at room temperature. The study indicates that to achieve high-performance high-electron mobility transistors, the surface roughness during processing is as critical as maintaining a sharp heterojunction.