Antimicrobial peptides (AMPs) represent a class of molecules synthesized by different organisms as an ancient innate defense mechanism against different pathogens like bacteria, fungi, viruses. Their characteristics make them good candidates to fight against bacteria together with or as an alternative to antibiotics. To decide on AMPs suitability for use in mammalian systems we redefined a ‘therapeutic index’ using the concentrations for which AMP is active against pathogens without inducing cytotoxic damage to the mammalian cells. Here we analyzed the toxic effects of eleven, highly active cationic AMPs towards human cells. The AMPs cytotoxicity was determined using common standardized assays measuring their effect on red blood cells (hemolytic index) and on lymphocytes (cell viability). The therapeutic index was calculated for all the AMPs tested. The highest therapeutic index was found for cecropins followed by magainins and the smallest for Melittin. For two peptides, Cecropin A which presents the highest therapeutic index and Melittin with the smallest therapeutic index we characterized in detail the cell death process distinguishing between apoptosis and necrosis. The toxic effects produced by Cecropin A and Melittin are induced mostly by means of apoptosis suggesting that the definition of therapeutic index has to consider the apoptotic effects of AMPs. Thus we provided here a unitary way to characterize the side effects of AMPs. The analysis of in vitro cytotoxic effects of AMPs using the global concept of therapeutic index can be a powerful way to decide which peptide can be taken for further testing in preclinical trials.