A combination of high-resolution X-ray diffractometry, Rutherford back scattering spectroscopy and secondary-ion mass spectrometry (SIMS) methods were used to characterize structural transformations of the damaged layer in Si(001) substrates heavily doped by Zn ions after a multistage thermal treatment. The shape of the SIMS profiles for Zn atoms correlates with the crystal structure of the damaged layer and depends on the presence of the following factors influencing the mobility of Zn atoms: (i) an amorphous/crystalline (a/c) interface, (ii) end-of-range defects, which are located slightly deeper than the a/c interface; (iii) a surface area enriched by Si vacancies; and (iv) the chemical interaction of Zn with Si atoms, which leads to the formation of Zn-containing phases in the surface layer.