Despite continuous advances, anticancer therapy still faces several technical hurdles such as selectivity on cellular and subcellular targets of therapeutics. Toward addressing these limitations, we have combined the use of proapoptotic peptides, cyanine dyes and folate to target the mitochondria of tumor cells. Hence, a series of proapoptotic peptides and their conjugates with a cyanine dye and/or a folate were prepared via solid-phase peptide synthesis (SPPS) and their activity tested in different mammalian cell lines. Compounds bearing either a cyanine dye or folate were found to be more cytotoxic than the parent peptides or more selective towards cells overexpressing the folate receptor α, which is commonly found on the surface of tumor cells. Nevertheless, constructs containing both components showed diminished potency and selectivity.