Polyisocyanopeptides have been synthesised containing acetylene groups on the side arms as scaffolds for multifunctional derivatisation by the copper-catalysed click reaction with a variety of azides. By using ethylene glycol azide and perylene azide chromophoric water-soluble polymeric nanowires (Mw 1–2 million Daltons) were formed. The potential to incorporate multiple chromophores was also demonstrated by the reaction of the acetylene-containing polymers with perylene azide and azidocoumarin dyes. In the latter case a blue-shifted emission of the coumarin was observed due to the interaction with the coupled perylene molecules. In particular the ability to form water-soluble dye-containing polymers, which can be modified by the addition of biomolecules, such as antibodies, proteins and peptides, give materials that are very promising as novel biomarker materials.