The interaction of two antimicrobial peptides (AMPs) with amphiphiles was investigated. In addition, the influence of sodium dodecyl sulfate (SDS) and cetyltrimethylammonium bromide (CTAB) solutions, both below and above the critical micelle concentration (cmc), was investigated by circular dichroism (CD) spectroscopy. The AMPs we used were from two different classes: C/S-Ar-1, from a lugworm, and LL-20, a fragment of human LL-37. Cationic CTAB did not influence the AMPs, independent of the amphiphile aggregation state. However, anionic SDS had a clear effect on the secondary structure of the peptides. In the case of C/S-Ar-1, no difference was observed in the CD spectra below or above the cmc (change to beta-sheet). In contrast, SDS monomers led to an aggregation of LL-20 and SDS micelles changed the secondary structure of the peptides from unstructured to alpha-helical.