In order to better understand the mechanisms of action of linear cationic host defense peptides, biophysical and structural investigations of their interactions with membranes and with other biomacromolecules are reviewed. In particular, an extensive overview will be given of the topological studies of magainins in a number of different lipid environments. Furthermore, amphipathic helices have been designed in such a manner to allow the easy control of their membrane alignment. These peptides not only exhibit potent antimicrobial and transfection activities, but their investigation has also provided important insights into mechanistic aspects of their biological functions. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.