Gas phase etching of silicon wafers with HCI at temperatures above 1200 K results in a surface which is either smooth or pitted, depending on temperature and HC1 input concentration. Whereas a smooth surface is the result of a steady flow of steps across the surface, etch pits are the result of a secondary, parallel etching reaction which creates “vacancies” in the surface. It is assumed that these vacancies cluster together to give microscopic holes in the silicon surface, that are large enough to be stable and that allow a vertical etching mechanism giving etch pit formation. It is shown, that the conditions needed for this etch pit formation depend largely on the local undersaturation of the main reaction product SiCl2, the diffusion velocity of vacancies in the silicon surface and the velocity of steps on the surface. Using this concept, a quantitative description for the origin of etch pits and an explanation for the experimentally found transition line between the smooth and pitted regions in the PHC1-T diagram are given, leading to an activation energy for vacancy diffusion in the surface of 70 kcal/mole.