Cationization of large polymers and their fragments on novel self-assembled monolayer substrates has been studied with time-of-flight secondary ion mass spectrometry (ToF-SIMS). Low (1 kDa) and high (400 kDa) molecular weight poly(ethylene oxide) (PEO) were spin-coated on metal ion substituted, carboxylic terminated, self-assembled monolayers on gold. Both cationized fragments and additional whole molecular species were observed for the 1 kDa PEO, while for 400 kDa PEO, only chain fragments of up to 30 monomer units were detected. Fragmentation pattern dependence on polymer molecular weight and the nature of the substrate is discussed. The intensity of the cationized fragments was found to depend on the metal ion used. Complementary experiments carried out on methyl terminated self-assembled monolayers suggested that metal ions that are desorbed from the gold surface, and therefore not in close proximity to the polymer, do not cationize polymers and their fragments. The substrates used in this work are simple to prepare, reproducible, and provide a model system for studies on the cationization of both polymers and proteins. Also, these ionically terminated self-assembled monolayer substrates open up new analytical possibilities for static SIMS.