Chiral isomers of 3-substituted polythiophenes with amino acid functiontionalized side chains are compared. The polymers show pH-dependent absorption, emission, and circular dichroism spectra in buffered aqueous solution. At pH equal to pI of the amino acid, the backbones adopt nonplanar helical conformations, and the polymer chains are separated from each other. Increasing pH leads to more planar conformations of the backbones and an aggregation of the polymer chains occurs. A lower pH will also lead to more planar conformation of the backbones, but aggregation of the polymer chains appears to be absent. The nonplanar to planar transition of the polymer backbone and the separation/aggregation of different polymer chains is not affected by stereochemistry of the zwitterionic side chain. The two isomers have almost identical pH-dependent absorption and emission spectra. However, the chirality of the zwitterionic side chain is reflected in the conformation of the polymer backbone, giving rise to a righthanded and left-handed helical form of polythiophene chains since the induced circular dichroism patterns of the two polymers are mirror images.