The secondary ion emission behavior of 10 different thiols (8 alkanethiols, with n=4–18 C atoms, TSA, and MCP) was investigated. In particular, we determined the generated negative secondary ion species Xi-, their yields Y, the corresponding damage cross section σ(Xi-), and the activation energy for desorption ED(Xi-) (from the temperature behavior) of these secondary ions. The results supply important information on the analytical capabilities of secondary ion mass spectrometry (e.g., sensitivity and ultimate lateral resolution), as well as on the capabilities and limits of ion beam induced modification of these molecular overlayers. By comparing spectra and yields for different thiols bonded in the same way to the same substrate, these results give some additional insight into the ion formation process. A comparison of the activation energy for desorption ED(Xi-) with the corresponding damage cross section σ(Xi-) supplies insight into the energy distribution within the impact cascade. © 2000 American Vacuum Society.