Development of the new antimicrobial agents against antibiotic resistance pathogens is the nowadays challenge. Antimicrobial peptides (AMP) occur as important defence agents in many organisms and offer a viable alternative to conventional antibiotics. Therefore they have become increasingly recognized in current research as templates for prospective antibiotic agents. The efficient designing of the new antimicrobials on the basis of antimicrobial peptides requires comprehensive knowledge on those general physical-chemical characteristics which allow to differ antimicrobial peptides from non-active against microbs ones. According to supposed mechanisms of action, AMP interact with and physically disrupt the bacterial membranes. Consequently, hydrophobicity, amphiphilicity and intrinsic aggregation propensities are considered as such major characteristics of the peptide, which determine the results of peptide-membrane interactions. For some kind of peptides such characteristics as hydrophobicity, amphiphilicity and aggregation bias determines their ability to compose transmembrane domain of the membrane protein, whilst for others the same properties are respond for their antimicrpobial activity, i.e. give them ability of membrane permeability and its damage. In this review we analyze the data about hydrophobicity, amphiphilicity and intrinsic aggregation propensities available in literature in order to compare antimicrobial and transmembrane peptides and show what is the common and what is the difference in this respect between them.