Self-assembled multilayers of the three modified cyclodextrins (hexakis(2,3-O-hexyl-6-deoxy-6-amino)-alpha-cyclodextrin (1), heptakis(2,3-O-hexyl-6-deoxy-6-amino)-beta-cyclodextrin (2), and octakis(2,3-O-hexyl-6-deoxy-6-amino)-gamma-cyclodextrin (3)) on bare gold, as well as on gold surfaces modified with mercaptopropionic (4) and mercaptooctanoic (5) acid, were investigated by cyclic voltammetric, contact angle, FT-IR, and quartz crystal microbalance measurements in neutral aqueous media. The level of organization of the aggregates formed by the three CD derivatives (1-3) on the negatively charged surface of the mercaptopropionic and mercaptooctanoic acid modified gold electrodes proved to be substantially better than that on bare gold electrodes. This finding suggests that although the amphiphilic character of compounds 1-3 can induce aggregation on a gold surface, the electrostatic interaction between the carboxylic acid groups and the positively charged cyclodextrins is the primary force leading to the formation of well-organized aggregates.