The synthesis and fluorescence behaviour of a range of amphiphilic poly(L-lysine co-bis-amine-Cy-3 iso-phthalamide) polymers that incorporate low levels of Cy-3 dye co-monomer (0.5-2.1 % (w/w)) in their backbone have been investigated in aqueous solution over a range of pH values. The desired functionality of these biocompatible, hydrophobically modified polyelectrolytes was achieved by incorporating pendant hydrophilic carboxyl groups along the polymer backbone, via the L-lysine moiety, balanced by a degree of hydrophobicity introduced via the iso-phthaloyl moiety. Thus, the polymer changes from an extended conformation at high degrees of ionisation to a compact conformation stabilised by hydrophobic association at low degrees of ionisation and eventually precipitates from solution. At intermediate degrees of ionisation, such polymers exhibit amphiphilic properties. A bis-functional cyanine fluorophore derivative, copolymerised within the polymer backbone, is demonstrated to act as a fluorescent reporter on the conformational state of the polymer. The materials have higher intrinsic fluorescence intensity per fluorophore monomer over a broad range of concentrations than bis-amine Cy-3 and their maximum fluorescence intensity is up to eight fold higher than the maximum intensity of bis-amine Cy-3, which is limited by quenching. It is also shown that the free fluorophore can be used to probe the conformation of unlabelled poly(L-lysine iso-phthalamide) through electrostatic interaction with the polymer. The technique allows rapid spectrophotometric determination of polymer conformation and offers the potential of an environmentally sensitive molecular pH probe for in vivo use. (C) 2003 Elsevier Ltd. All rights reserved.