Despite their great potential, gene delivery polyplexes have a number of limitations, including their tendency for aggregation in vivo or upon storage. In previous studies, we could show that hydroxyethyl starch (HES)-decoration of polyplexes reduces aggregation in vitro and in vivo. The current study investigates the ability of HES-decoration to improve the stability of polyplexes upon storage as frozen-liquid or lyophilizate, and uses naked polyplexes or PEGylated ones as controls. For this purpose, freeze-thaw (FT) experiments of the polyplexes were conducted in the presence of standard excipients (glucose, sucrose or trehalose). Dynamic light scattering (DLS) measurements showed that HES-decoration imparted better stability when glucose was used, while both HES and PEG were effective in inhibiting aggregation in the presence of trehalose or sucrose. In contrast, the lyophilized HES-coated polyplexes were more stable than the PEGylated ones as shown by DLS, even after storage for 10 weeks at an elevated temperature. Evaluation of the gene transfer efficiency of the stored samples showed no negative effect of storage, except for the lyophilized naked polyplexes. In general, this study shows that, while both HES- or PEG-coats could prevent aggregation under frozen-liquid storage, the HES-coat resulted in superior protective effect upon lyophilization, with possible advantages for in vivo application. In summary, our developed HES-coats provided effective cryo- and lyoprotection to the DNA polyplexes.