Historical experiments in molecular (organic) secondary ion mass spectrometry (SIMS) at keV energies are reviewed, including the first matrix experiments and the introduction of key mechanistic concepts. The paper deals principally with the newer topic of ion/surface collisions at lower energies (hyperthermal energies, 1-100 eV). Chemically relevant processes occurring in this regime include surface-induced dissociation (SID) as a means of activating and fragmenting organic ions, chemical sputtering used for surface analysis, reactive collisions as a means of surface chemical modifications, and ion soft-landing at surfaces which amongst other things allows preparative mass spectrometry. Fundamentals of great interest include studies of energy partitioning during inelastic collisions and non-statistical dissociation mechanisms. Unique applications of ion/surface collisions include the creation of protein arrays by ion soft-landing. (C) 2004 Elsevier B.V. All rights reserved.