Amino acids and peptides (di- and tripeptides) as chemically bonded ligands in liquid chromatography were investigated. The comparison between 9 home-made amino acid- and peptide-silica stationary phases in hydrophilic interaction liquid chromatography (HILIC) and reversed-phase liquid chromatography (RP HPLC) systems has been presented. The investigated stationary phases were modified by the following amino acids: phenylalanine, leucine, alanine, glycine, and aspartic acid. Desired interactions were derived from the retention variation between pairs of similar solutes differing with particular structure properties. In the case of HILIC mode, the characterization was performed in terms of the degree of hydrophilicity, selectivity for hydrophilic–hydrophobic compounds, selectivity for the regio and configurational substituents, anion and cation exchange properties, and acidic or basic nature of the stationary phase surface. Under RP HPLC conditions, following features were elucidated: hydrophobicity, hydrophobic selectivity, shape selectivity, hydrogen bonding, electrostatic interactions at pH values 2.7 and 7.6. The results of the selectivity for partial structural differences were presented as radar-shaped plots and in tabular format. The factor analysis (FA) based on the principal component analysis (PCA) was also used in the stationary phase comparison. The performed research assisted in the evaluation of the relation between the chemical properties of bonded amino acid sequence and their role in the retention mechanism.