A combination of two model approaches was used to explore the nature of silicone–protein interactions. Phage display technology was used to present a combinatorial library of peptides, in this case the phage library PhD.-12, to a series of model silicone surfaces. Solid, molecular cage silsesquioxanes were used as the models for silicone surfaces. The silsesquioxanes were octamethyloctasilsesquioxane (methyl8-T8), octaphenyloctasilsesquioxane (phenyl8-T8), octahydridooctasilsesquioxane (H8-T8) and dodecatrifluoropropyldodecasilsesquioxane (trifluoropropyl12-T12). The first two silsesquioxanes bear simple aliphatic (Me) and aromatic (Ph) pendant groups, and are simple silicone analogues. The second two silsesquioxanes have functionalised pendant groups, H and CF3CH2CH2. The panning results, using a wild-type phage as a control, show that the phage library binds to the simple aliphatic and aromatic silsesquioxanes strongly but non-specifically, and largely through the protein coat on the phage. The functionalised silsesquioxanes (H and CF3CH2CH2) are bound specifically by the phages. A statistical analysis of the DNA sequences of the strongly binding phages was carried out. The peptides that bind to H8-T8 are strongly enriched in proline content at positions 7 and 8, with enhanced histidine at positions 5 and 9, and enhanced threonine at position 11. The proline residues presumably induce a favourable conformation in the peptide for binding to the silsesquioxane surface. The enhanced histidine content is significant. It has been known for many years that imidazole has a particular affinity for electrophilic silanes. The amino acid distribution for trifluoropropyl12-T12 binding peptides is markedly different from that of H8-T8 silsesquioxane. Proline is again enhanced, but in positions 4, 11 and 12, and there are also very high concentrations of serine in positions 1, 9 and 11, and threonine in positions 1, 2 and 12. The highly polar nature of the CF3 group is likely to engage in hydrogen bonding with the OH groups of the serine and threonine side chains, accounting for the tight binding to trifluoropropyl12-T12 silsesquioxane.