The lipid bilayer, which comprises all cell membranes, represents a formidable barrier to the delivery of large hydrophilic molecules into cells. The ability to introduce information-rich molecules into cells is a challenge in the development of new therapeutics for diseases not currently amenable to small molecule intervention. This work focuses on the delivery of peptide-based molecules including; inhibitors, substrates and carriers into cells. A series of peptide-based inhibitors against caspase-3, an intracellular enzyme involved in apoptosis, were assessed for their cell membrane permeability. Proteolytic activation of a cell penetrating peptide was also investigated as a means of controlling the uptake of these carrier peptides into cells. Finally, the uptake and processing of an internally quenched Tat-caspase substrate was examined in cells undergoing apoptosis. This book may be of interest to scientists working in any area where large molecules need to be effectively delivered to cells. It may be of particular interest to those working on cell penetrating peptides, proteases or apoptosis.