A method for controlling the autodoping during epitaxial silicon deposition. First, the substrate (10) is cleaned to remove any native oxide. After being cleaned, the substrate (10) is transferred to the deposition chamber in an inert or vacuum atmosphere to inhibit the growth of a native oxide on the surface of the wafers. A lower temperature (i.e., 500-850.degree. C.) capping layer (14) is deposited to prevent autodoping. Then, the temperature is increased to the desired deposition temperature and the remainder of the epitaxial layer (18) is deposited.