The ability of Bin+ cluster ion sources to provide information about the physical structure of an integrated film composed of oligonucleotides and non‐nucleic acid oligomers of poly(2‐hydroxyethyl methacrylate) (PHEMA) has been explored using static time‐of‐flight (ToF) SIMS (ToF‐SIMS). Fragment intensities from PHEMA and oligonucleotides were compared. Negative ion spectra indicated that the Bi5+ source provided details that were either not apparent or at much reduced sensitivity when using Bi3+ and Bi+ sources. The Bi3+ ion source provided higher secondary ion intensities for positive ion fragments, and more than 200‐fold selectivity for ionization of oligonucleotide in comparison to PHEMA when in mixture, even though the oligonucleotides were not immobilized as a coating superimposed on PHEMA. Copyright © 2010 John Wiley & Sons, Ltd.