An intrinsic defect may exist in thin gate oxides. Such a defect can increase the leakage current in a manner similar to stress-induced leakage current. In this paper, we have shown that the effect of this intrinsic defect can be greatly reduced by in situ removal of the native oxide followed by growing a high-quality thermal oxide. By using such in situ cleaning, ultrathin oxides can be prepared with atomically smooth interfaces, good thickness uniformity, and reduced leakage currents.