In response to transmembrane potentials which are negative on the inner side of both the plasma and mitochondrial membranes, cationic dyes displaying appropriate structural features naturally accumulate in the cytosol and inside the mitochondria. Because enhanced mitochondrial membrane potential is a prevalent tumor cell phenotype, a number of cationic dyes preferentially accrue and are retained for longer periods in the mitochondria of tumor cells as compared to normal cells. The opportunities brought about by this phenomenon in chemo- and photochemotherapy of neoplastic diseases is highlighted by the observation that the phototoxic effects associated with some of the cationic photosensitizers known to accumulate in cell mitochondria are much more pronounced in tumor cells than in normal cells. However, the structural determinants of selective phototoxicity towards tumor cells are not well understood, and the lack of a robust model to describe the relationship between molecular structure and tumor selectivity has prevented mitochondrial targeting from becoming a more dependable therapeutic strategy. In this report we describe how the lipophilic/hydrophilic character of a series of cationic triarylmethane dyes affects the selectivity with which these photosensitizers mediate the destruction of tumor cells. Our results indicated that only the more hydrophilic triarylmethanes show tumor selectivity, presumably because these are the only dyes capable of staining energized mitochondria with a high degree of specificity. The partition of the more lipophilic dyes into a variety of extra-mitochondrial subcellular compartments occurs with comparable efficiencies in tumor and in normal cells, and this less specific subcellular localization precludes tumor selectivity from taking place.