Absorption, distribution, metabolism, and excretion (ADME) properties are of invaluable importance to a bioactive compound. Permeation process is one of the most widely studied by many different techniques. Among them, reversed-phase liquid chromatography (RP-LC) is proving to be of great interest, in which retention time can provide some insights on the hydrophobic interaction behavior. A series of antiprotozoal meso-ionic 1,3,4-thiadiazolium-3-aminides were studied in order to obtain the retention-time data through two different organic modifiers using a commercially available Supelcosil ABZ(+) Plus column. MeOH/buffer mobile phase provided the best results in assessing the hydrophobicity of these compounds as compared to MeCN. Quantitative Structure-Retention Relationships (QSRR) models were built to identify the physicochemical properties that govern the process by using PLS analysis. VolSurf descriptors extracted from water (H(2)O), hydrophobic (DRY), amide N-atom (N(1)) and carbonyl O-atom (O) probes showed that the retention is positively correlated to the molecules size and shape, hydrophobic pattern, and dispersion forces. Hydrogen bonding depicts the solvent force considering the donor and acceptor differences between MeOH and MeCN organic modifiers.