The pH-dependent loading and release behavior of small hydrophilic molecular probes in polyallylamine and hyaluronic acid multilayer films was investigated. These studies were carried out using the water-soluble dyes Indoine Blue and Chromotrope 2R, and their loading and release profiles were followed with UV-vis spectroscopy. The results of these studies suggest that the incorporation and release of material from such films depend on the degree of film swelling, the ability of the dye molecules to aggregate in the film, as well as the attractive and repulsive interactions occurring between the probe molecules and the acid-base functional groups in the films. Both the degree of dissociation of the acid-base functional groups and the extent of film swelling are pH-sensitive. As a result, the amount of each dye incorporated in the film also depends on the pH conditions, with a maximum loading capacity of 3.8 x 10(-3) mg/cm(3) of Chromotrope 2R and 5.7 x 10(-2) mg/cm(-3) of Indoine Blue. In turn, we found that by manipulating the pH of the release solution it is possible not only to control the rate of the release of the molecular probes but also to regulate the amount of probe material released. In fact, completely trapping the incorporated probes in the multilayer films was also successfully demonstrated. These findings can be rationalized by examining the interactions of the dye molecules with the polyelectrolytes, the ability of molecules to form J-aggregates, and pH-dependent physicochemical properties of the multilayer system, such as the acid-base equilibria of the polyelectrolytes and the swelling behavior of the films. It is believed that this information is fundamentally important to understanding of how to effectively manipulate the films for potential controlled release applications.