A theoretical and experimental study on the iodination of BODIPY dyes with different degrees of substitution has been developed. Polyhalogenated BODIPYs synthesized in this work are the first examples of this type of dyes with more than two halogen atoms in the BODIPY core and they can be selectively functionalized. Surprisingly, the position in which halogen is attached has a marked effect in the photophysical properties and modulates the fluorescence capacity of the resulting BODIPY. These iodinated BODIPYs are efficient singlet oxygen generators.