The acid dissociation constant is one of the fundamental properties of organic molecules. In this study, den- sity functional theory (DFT) calculations with B3LYP combined with 6-31+G(d) basis set were applied for determination of acidic dissociation constants of L-phenylalanyl-glycine and L-alanyl-L-alanine. An ab initio procedure for accurately calculating aqueous-phase pKa values of the L-phenylalanyl-glycine and L-alanyl- L-alanine is presented. Formation of intermolecular hydrogen bonds between the existent species and water has been analyzed using Tomasi’s method. In this way, it was determined that in alkaline aqueous solutions the cation, anion, and neutral species of L-phenylalanyl-glycine and L-alanyl-L-alanine are solvated with some molecules of water. Furthermore, the correlation between the pKa values of these dipeptides was investigated theoretically, and a comparable agreement was found with the experimental results.