Up to now, the analysis of organic or biological samples was mainly investigated using static SIMS, while dynamic SIMS was generally limited to the analysis of inorganic samples. The increasing sophistication of organic optoelectronic devices (e.g. organic light emitting diodes and organic photovoltaic cells, etc.) requires molecular-level dimensional control in the fabrication of multilayered structures with specifically engineered interfaces. However, analytical tools for monitoring such fabrication precision are scarce. In a current project, we address this challenge by advancing the development of low-energy Secondary Ion Mass Spectrometry (LE-SIMS) for the analysis of organic-based optoelectronic materials systems.In the present work, we investigate the fragmentation as well as the ionization mechanisms for several molecules used in such devices: fullerene, copper phthalocyanine and tris(8-hydroxyquinolinato) aluminium have been deposited onto silicon wafers. The study has been carried out on a Cameca SC-Ultra instrument under Cs + bombardment for various impact energies in the M − mode. Constant M − secondary ion intensities have been observed throughout the organic layers for some characteristic fragments of the organic molecules.