Surfaces exhibiting antimicrobial activity were prepared for potential medical application. A polycationic lipopeptide polymyxin B was selected as the bioactive agent for covalent immobilization onto the surface. First, by using sol–gel technology the inert glass substrate was functionalized by a silane coating with epoxide rings to which the peptide was coupled by means of a catalyst. Preparation of the coating and presence of the peptide on the surface were followed by FTIR, XPS and AFM analyses. The obtained material showed antimicrobial effect indicating that in spite of immobilization the peptide has retained its bioactivity. The coated surface was able to reduce bacterial cell counts of the Gram-negative bacterium Escherichia coli by more than five orders of magnitude in 24 h of incubation. It can be concluded that bioactive coatings with covalently bound polycationic peptides have potential for application on medical devices where leakage into the surrounding is not allowed in order to prevent bacterial growth and biofilm formation.