Provided is a method of fabricating a CMOS transistor in which, after a polysilicon layer used as a gate is formed on a semiconductor substrate, a photoresist pattern that exposes an n-MOS transistor region is formed on the polysilicon layer. An impurity is implanted in the polysilicon layer of the n-MOS transistor region using the photoresist pattern as a mask, and the photoresist pattern is removed. If the polysilicon layer of the n-MOS transistor region is damaged by the implanting of the impurity, the polysilicon layer of the n-MOS transistor region is annealed, and a p-MOS transistor gate and an n-MOS transistor gate are formed by patterning the polysilicon layer. The semiconductor substrate, the p-MOS transistor gate and the n-MOS transistor gate is cleaned with a hydrofluoric acid (HF) solution, without causing a decrease in height of the n-MOS transistor gate.