The aim of this study is to assess the insights of molecular properties of the xanthene dyes [fluorescein (FL), Rose Bengal (RB), erythrosin B (EB), and eosin Y (EY)] to correlate systematically their photodynamic efficiency as well as their phototoxicity against a carcinoma cell line. The phototoxicity was evaluated by comparing the values of the medium inhibitory concentration (IC50) upon HEp-2 cells with the xanthene corresponding photodynamic activity using the uric acid as a chemical dosimeter and their octanol-water partition coefficient (log⁡P). RB was the more cytotoxic dye against HEp-2 cell line and the most efficient photosensitizer in causing photoxidation of uric acid; nevertheless it was the only one characterized as being hydrophobic among the xanthenes studied here. On the other hand, it was observed that the halogen substituents increased the hydrophilicity and photodynamic activity, consistent with the cytotoxic experiments. Furthermore, the reactivity index parameters, electric dipole moment, molecular volume, and the frontier orbitals were also obtained by the Density Functional Theory (DFT). The lowest dipole moment and highest molecular volume of RB corroborate with its highest hydrophobicity due to heavy atom substituents like halogens, while the halogen substituents did not affect expressively the electronic features at all.