Two series (degree of polymerization: 20-200) of polylysines with Z and TFA protecting groups were synthesized, and their behavior in a range of analytical methods was investigated. Gel permeation chromatography of the smaller polypeptides reveals a bimodal distribution, which is lost in larger polymers. With the help of GPC, NMR, circular dichroism (CD), and MALDI-TOF, it was demonstrated that the bimodal distribution is not due to terminated chains or other side reactions. Our results indicate that the bimodality is caused by a change in secondary structure of the growing peptide chain that occurs around a degree of polymerization of about 15. This change in, secondary structure interferes strongly with the most used analysis method for polymers GPC by producing a bimodal distribution as an artifact. After deprotection, the polypeptides were found to exhibit exclusively random coil conformation, and thus a monomodal GPC elugram was obtained. The effect can be explained by a 1.6-fold increase in the hydrodynamic volume at the coil helix transition. This work demostrates that secondary structures need to be carefully considered when performing standard analysis on polypeptidic systems.