Despite their potent antimicrobial activity, the usefulness of antimicrobial peptides (AMPs) as antibiotics has been limited by their toxicity to eukaryotic cells and a lack of stability in vivo. In the present study we examined the effects of introducing D-lysine residues into a 15-residue hybrid AMP containing residues 1–7 of cecropin A and residues 2–9 of melittin (designated CM15). Diastereomeric analogs of CM15 containing between two and five D-lysine substitutions were evaluated for their antimicrobial activity, lysis of human erythrocytes, toxicity to murine macrophages, ability to disrupt cell membranes, and protease stability. All of the analogs caused rapid permeabilization of the Staphylococcus aureus cell envelope, as indicated by uptake of SYTOX green. Permeabilization of the plasma membrane of RAW264.7 macrophages was also observed for CM15, but this was substantially diminished for the D-lysine containing analogs. The introduction of D-lysine caused moderate decreases in antimicrobial activity for all analogs studied, with a much more pronounced reduction in toxicity to eukaryotic cells, leading to marked improvements in antimicrobial efficacy. Circular dichroism studies indicated a progressive loss of helical secondary structure upon introduction of D-lysine residues, with a good correspondence between helical content and eukaryotic cell cytotoxicity. Overall, these studies indicate that disruption of amphipathic secondary structure reduces both antimicrobial activity and eukaryotic cell toxicity, but that the reduction in eukaryotic cell cytotoxicity is more pronounced, leading to an overall gain in antimicrobial selectivity.