The effect of linker stability on the intracellular localization and apoptotic activity of cytochrome c (Cyt c) conjugated to an amphipathic cell-penetrating peptide (CPP), model amphipathic peptide (MAP), was tested in HeLa cells. While conjugates linked with a stable thioether cross-linkage were only found in the vesicular compartment, a portion of the conjugate linked with a reducible disulfide bond was also detected in the cytosol. The apoptotic function of the reducible and non-reducible Cyt c-MAP conjugates was also evaluated quantitatively using the caspase 3 and annexin V/propidium iodide detection assays in the presence of a proteasome inhibitor used to inhibit cytosolic Cyt c degradation. Analysis for early phase apoptosis revealed that linker stability was important for biological activity. Only the reducible disulfide-linked Cyt c-MAP conjugate, and not free Cyt c or thioether-linked Cyt c-MAP, initiated apoptosis in proteasome-inhibited cells which correlated with the cytosolic localization profiles of the proteins. The co-treatment of disulfide-linked Cyt c-MAP with a disulfide reduction inhibitor decreased the amount of Cyt c delivered to the cytosol, which correlated with a lack of apoptotic activity. These findings indicated the presence of a vesicle-to-cytosolic delivery process for disulfide-linked MAP conjugates, which can be used to improve CPP-based drug delivery systems transporting cargo to cytosolic sites.