LL-37 is the only cationic peptide belonging to the cathelicidin family expressed in humans. LL-37 has bactericidal activity and exerts immunomodulatory functions, thus forming, together with other peptides, the first line of defense against infections. The formation of LL-37 aggregates in the presence of neutral membranes promotes lack of specificity for microbial cells, which could explain why LL-37 becomes cytotoxic towards eukaryotic cells at high concentrations. Cationic amino-acids such arginine (Arg) and lysine (Lys) are known determinants for bacterial killing; however very little is known about how Lys-Arg exchange can influence LL-37 biological activities. Since antimicrobial peptides are promising candidates for the development of novel anti-infective agents, we have compared the bactericidal and cytotoxic effects of five LL-37 variants with wild-type peptide. The bactericidal activity was tested against Escherichia coli and Streptococcus agalactiae, while cytotoxicity was measured against A549, a human bronchoepithelial cell line. We found clear differences in bacterial killing kinetics towards both pathogens when central Arg residues were mutated in Lys, with Arg more efficient than Lys in bacterial membrane permeation. Of interest, the Arg at position 34 can compensate for the absence of the Arg at position 19 and 23 and the presence of Lys at the other positions resulted in a diminished toxicity for eukaryotic cells. Our study sheds new light on key amino-acid residues of LL-37 and should be considered when novel cationic amphipathic peptides derived from LL-37 are designed.