Heavy metal atoms (such as Cu) spontaneously undergo a dissolution reaction when they come into contact with silicon. Most investigations in this extensively studied area begin with a clean, bare wafer and focus on metal contamination during the IC manufacturing stage. In this work, the effect of Fe and Cu contamination on raw wafers was elucidated. When two batches of raw wafers are scheduled, one uncontaminated and one with various degrees of contamination ranging from 0.1 to 10 ppb undergo the typical steps of the 90 nm LOGIC complementary metal–oxide–semiconductor (CMOS) semiconductor manufacturing process. The main contribution of this work is the discovery of a previously unidentified cause of gate oxide leakage: the formation of tiny holes by metal contamination during the wafer manufacturing stage. Because tiny holes are formed, a spontaneous reaction can occur even with at very low metal concentration (0.2 ppb), revealing that the wafer manufacturing stage is more vulnerable to metal contamination than the IC manufacturing stage and therefore requires stricter contamination control.