The research program incorporated latest scientific trends which aim to increase quality, efficacy and safety of medicines. Research on drug delivery systems, which holds the central role of this program, remains of crucial importance for the development of a new chemical entity with proven pharmacological activity into a potential drug product. The developed methodology can be successfully implemented to research on classic low-molecular weight molecules, as well as to peptides and proteins and hydophilic metabolically unstable molecules which in unchanged form poorly pass various physical and biological barriers. The majority of therapeutics, used in the treatment of cardiovascular diseases, cancer, chronic inflamations and infectios diseases belong to this classes of drugs. Collaboration in the development of medicines for treatment of these disease states, which represent the vast social burden, remain the core of our research program. Within the scope of this program, model drugs were studied in multiphase systems. Various hydrophilic, lipophilic and amphiphilic drugs were incoprporated into nanoparticles. The major finding of this research was that lipophilic and hydrophilic domains represent the decisive system for location of the drug in the colloidal carriers and therefore affect drug entrapment efficacy, drug stability and bioavailability and consequently drug biological effects. Rheological analysis basing on non-destructive oscilatory rheometry was succesfully applied to the structure elucidation in the study of semisolid emulsion systems. Furthermore, properties of microspheres as a potential drug delivery system for intravesical application were investigated. Optimal characteristics, critical for their mucoadhesion and penetration of the incorporated drug into the bladder mucosa were defined. Moreover, features of the urinary bladder affecting local administration of the drug delivery system in the bladder were examined as well. With our research it was clarified that physicochemical properties such as solubility and logP do not represent reliable predictors for drug absorption. Therefore, diffusion model which enables the investigation of drug transport through biological barriers was developed and applied in the study with monocarboxylic acids. Pharmacokinetic-pharmacodynamic modeling methodology was developed and applied into the analysis of LADMER processes, which influence the rate, intensity and duration of drug effects. The insights acquired in the study of mechanisms and kinetics of drug transport and interactions in the biological systems disclose new possibities for rational development of medicines.