It is known that cyclodextrins (CDs) extract lipid components from bilayer of liposomes. This could undermine the potential benefits of liposomes as drug carriers. In this study, we demonstrated that PC-Chol liposomes with various CDs or rhapontin (Rh)-hydroxypropyl betaCD (HPbetaCD) complexes could be stabilized by association with the amphiphilic polyelectrolyte, poly(methacrylic acid-co-stearyl methacrylate). Based on the results of differential scanning calorimetry, photocorrelation spectroscopy and transmission electron microscopy, the polymer-associated liposomes had the same vesicular form as liposome with clear boundaries and retained structural integrity for at least 1 month. In addition, the polymer-associated structure was unaffected by the type of CD, the composition and concentration of lipid components, and the concentration of the Rh-HPbetaCD complex. This contrasted with PC-Chol liposomes, whose structure was dependent on these factors. Using structurally different polymer-associated liposomes and PC-Chol liposomes containing the Rh-HPbetaCD complex, we also showed that the stability of vesicles could influence the skin permeability of CD-drug complexes.