Molecular properties relevant to pharmacokinetics of two sets of newly synthesized hydantoin derivatives based on two well-known drugs (Nirvanol and Phenytoin) were studied. Properties under consideration were either determined empirically by reversed-phase high-performance thin-layer chromatography or calculated by the use of established theoretical medicinal chemistry/drug design software. These properties represent selected structural features of analytes, which affect their processes of absorption, distribution, metabolism, excretion, and toxicity. Principal component analysis was used to visualize the differences between six mobile phase modifiers used as well as similarities between 24 analyzed compounds. To find appropriate quantitative relationships between R M, W for the tested compounds and molecular descriptors, stepwise regression, partial least squares (PLS), and robust PLS were used. The best results were obtained with robust PLS.