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The photodynamic antimicrobial chemotherapy (PACT) activities of four meso-pentafluorophenylBODIPY dyes were studied against Staphylococcus aureus to identify structure-property relationships related to the introduction of different substituents on the BODIPY core. 1,3,5,7-Tetramethyl dyes with bromine and iodine atoms at the 2,6-positions (2a and 3a) were synthesized and characterized along with 3,5-dimethyl dyes that were either tetrabrominated at the 1,2,6,7-positions (2b) or diiodinated (3b) at the 2,6-positions. The incorporation of iodine atoms on the BODIPY core at the 2,6-positions enhanced the PACT activity relative to those of the di- and tetrabrominated dyes. Replacing the methyl groups at the 1,7-positions with protons to form 3b results in greater PACT activity than is the case with 3a since the absence of steric hindrance related to methyl groups at the 1,7-positions allows the meso-aryl ring to rotate closer to the plane of the [Formula: see text]-system of the BODIPY core. The tetrabrominated dye was found to have the lowest PACT activity due to a lack of stability in solution and poor uptake by the bacteria being studied. The electron-withdrawing pentafluorophenyl group was selected to lower the dipole moment of the BODIPY core dye since poor PACT activity was observed when a 2,6-dibromo-1,3,5,7-tetramethyl BODIPY dye was prepared with a thiomethylphenyl group (2c).