A mechanism for SiCl2 formation and desorption in the etching of Si(100)-(2×1) at low chlorine coverages is analyzed using first-principles calculations. We find that the two monochlorinated Si atoms of a surface dimer can rearrange into a metastable SiCl2(a) adsorbed species plus a Cl-free Si atom. Desorption of SiCl2 occurs via a two-step mechanism, in which the adsorbed species is preliminarily stabilized by the diffusion away of the free Si atom. The energy barrier to form SiCl2(a) is lower on a dimer next to a dimer vacancy than in an undamaged region of the surface, consistent with recent STM observation of preferential linear growth of etch pits along dimer rows.